EP4181954A1 - Immunogene sars-cov-2-zusammensetzungen, impfstoffe und verfahren - Google Patents

Immunogene sars-cov-2-zusammensetzungen, impfstoffe und verfahren

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Publication number
EP4181954A1
EP4181954A1 EP21746673.9A EP21746673A EP4181954A1 EP 4181954 A1 EP4181954 A1 EP 4181954A1 EP 21746673 A EP21746673 A EP 21746673A EP 4181954 A1 EP4181954 A1 EP 4181954A1
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EP
European Patent Office
Prior art keywords
cov
sars
seq
protein
cells
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
EP21746673.9A
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English (en)
French (fr)
Inventor
Pierre Charneau
Min-Wen KU
Pierre Authie
Nicolas Escriou
Maryline BOURGINE
Laleh Majlessi
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Institut Pasteur de Lille
Theravectys SA
Original Assignee
Institut Pasteur de Lille
Theravectys SA
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Priority claimed from PCT/IB2021/000293 external-priority patent/WO2022167831A1/en
Application filed by Institut Pasteur de Lille, Theravectys SA filed Critical Institut Pasteur de Lille
Publication of EP4181954A1 publication Critical patent/EP4181954A1/de
Pending legal-status Critical Current

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/12—Viral antigens
    • A61K39/215—Coronaviridae, e.g. avian infectious bronchitis virus
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/12—Viral antigens
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/86—Viral vectors
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/525—Virus
    • A61K2039/5256—Virus expressing foreign proteins
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/54—Medicinal preparations containing antigens or antibodies characterised by the route of administration
    • A61K2039/541—Mucosal route
    • A61K2039/543—Mucosal route intranasal
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/54—Medicinal preparations containing antigens or antibodies characterised by the route of administration
    • A61K2039/541—Mucosal route
    • A61K2039/544—Mucosal route to the airways
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/57—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2
    • A61K2039/575—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2 humoral response
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/20011—Coronaviridae
    • C12N2770/20034—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2810/00—Vectors comprising a targeting moiety
    • C12N2810/50—Vectors comprising as targeting moiety peptide derived from defined protein
    • C12N2810/60—Vectors comprising as targeting moiety peptide derived from defined protein from viruses

Definitions

  • SARS-COV-2 IMMUNOGENIC COMPOSITIONS, VACCINES, AND METHODS BACKGROUND
  • SARS-CoV-2 Severe Acute Respiratory Syndrome beta-coronavirus 2
  • MERS Middle East Respiratory Syndrome
  • lung is the organ of predilection for SARS-CoV-2, its neurotropism, like that of SARS-CoV and Middle East Respiratory Syndrome (MERS)-CoV, (Glass et al., 2004; Li et al., 2016; Netland et al., 2008) has been reported (Aghagoli et al., 2020; Fotuhi et al., 2020; Hu et al., 2020; Liu et al., 2020; Politi et al., 2020; Roman et al., 2020; von Weyhern et al., 2020; Whittaker et al., 2020).
  • MERS Middle East Respiratory Syndrome
  • ACE2 Angiotensin Converting Enzyme 2
  • COVID-19 human patients can present symptoms like headache, myalgia, anosmia, dysgeusia, impaired consciousness and acute cerebrovascular disease (Bourgonje et al., 2020; Hu et al., 2020; Mao et al., 2020).
  • Viruses can gain access to the brain through neural dissemination or hematogenous route (Desforges et al., 2014).
  • Coronaviruses are enveloped, non-segmented positive-stranded RNA viruses, characterized by their envelop-anchored Spike (S) glycoprotein (Walls et al., 2020).
  • SARS-CoV-2 S is a (180 kDa) 3 homotrimeric class I viral fusion protein, which engages the carboxypeptidase Angiotensin-Converting Enzyme 2 (ACE2), expressed on host cells.
  • ACE2 Angiotensin-Converting Enzyme 2
  • the monomer of S CoV-2 protein possesses an ecto-domain, a transmembrane anchor domain, and a short internal tail.
  • S CoV-2 is activated by a two-step sequential proteolytic cleavage to initiate fusion with the host cell membrane.
  • S CoV-2 - ACE2 interaction which leads to a conformational reorganization, the extracellular domain of S CoV-2 is first cleaved at the highly specific furin 682 RRAR 685 (SEQ ID NO: 99) site (Guo et al., 2020; Walls et al., 2020), a key factor determining the pathological features of the virus, linked to the ubiquitous furin expression (Wang et al., 2020).
  • the resulted subunits are constituted of: (i) S1, which harbors the ACE2 Receptor Binding Domain (RBD), with the atomic contacts restricted to the ACE2 protease domain and also harbors main B-cell epitopes, targeted of NAbs (Walls et al., 2020), and (ii) S2, which bears the membrane-fusion elements.
  • S1 which harbors the ACE2 Receptor Binding Domain (RBD)
  • RBD ACE2 Receptor Binding Domain
  • one or several host proteases including furin, trypsin, cathepsins or TransMembrane Protease Serine Protease (TMPRSS)-2 or -4, can be involved in this second cleavage step (Coutard et al., 2020).
  • TMPRSS TransMembrane Protease Serine Protease
  • the consequent “fusogenic” conformational changes of S result in a highly stable postfusion form of S CoV- 2 that initiates the fusion reaction with the host cell membrane (Sternberg and Naujokat, 2020) and lead to the exposure of a Fusion Peptide (FP), adjacent to S2'.
  • FP Fusion Peptide
  • lentiviral vectors exist under integrative (ILV) and non- integrative (NILV) forms which are permissive to insertion of up to 8kb-length transgenes of vaccinal interest and possess outstanding potential of gene transfer to the nuclei of host cells (Di Nunzio et al., 2012; Hu et al., 2011; Ku et al., 2020; Zennou et al., 2000).
  • ILV integrative
  • NILV non- integrative
  • LV coding for: (i) full-length, membrane anchored form of S (LV::S FL / LV::SFL), (ii) S1-S2 ecto-domain, without the transmembrane and internal tail domains (LV::S1-S2), (iii) S1 alone (LV::S1), (iv) mutated S deleted of a sequence encompassing the furin site and substituted at residues K 986 P and V 987 P to introduce consecutive proline residues in S2 (2P mutation) (LV::S ⁇ F2P ) thereby providing a stabilized (2P) and prefusion ( ⁇ F) form of the protein were generated.
  • LV coding for: (i) the spike protein of variant B1.351 (so called South African or ⁇ variant), (ii) the spike protein of variant B1.1.7 (so called UK or ⁇ alpha variant), (iii) the spike protein of variant B1.351 substituted at residues K 986 P and V 987 P, (iv) the full-length, membrane anchored form of S combined with a D614G substitution (LV::S FL -D614G), and (v) the spike protein of variant P.1 (so called Manaus or gamma variant).
  • the data presented in the examples establish in particular that LV::SFL and LV::S ⁇ F2P either in the integrative or non integrative version of the vector(i) induced neutralizing antibodies specific to the Spike glycoprotein (S) of SARS-CoV-2, the etiologic agent of COVID-19, with neutralizing activity comparable to those found in a cohort of SARS-CoV-2 patients, and (ii)
  • transgenic mice generated as a preclinical model showing unprecedent permissibility to SARS-CoV-2 replication including in brain the inventors were able to demonstrate that a LV encoding a prefusion form of spike glycoprotein of SARS-CoV-2 such as LV::S ⁇ F2P induces substantial protection of respiratory tracts and CNS against SARS-CoV-2.
  • the generated transgenic mice enabled addressing the capability of protection of the CNS by the developed LV encoding the Spike protein or a derivative or a fragment thereof according to the definition provided below and illustrated in the experimental examples.
  • the inventors have demonstrated that a single intranasal administration of a LV encoding a prefusion form of Spike glycoprotein of SARS-CoV-2 induces substantial protection of respiratory tracts and totally avoids pulmonary inflammation in the susceptible hamster model.
  • the upper respiratory tract mucosal boost/target immunization with LV::S FL or with LV::S ⁇ F2P was instrumental in the protection efficacy in stringent preclinical model constituted by the generated transgenic mice.
  • the presented virological, immunological and histopathological data demonstrates: (i) marked prophylactic effects of a LV-based vaccination strategy against SARS-CoV-2, (ii) the fact that LV-based immunization represents a promising strategy to develop vaccine candidates against coronaviruses, and (iii) mucosal immunization enables vigorous protective lung immunity and protective CNS immunity.
  • lentiviral vector in any of its forms harboring the lentiviral sequences essential for targeting host cells and enabling expression of a transgene, for instance encoding the Spike protein of SARS-CoV-2 or a derivative or fragment thereof bearing B epitopes and T epitopes, has shown capability to induce and/or activate immune response against the transgene antigen.
  • the inventors have in particular proven the capability of the lentiviral vector to retain or support a conformation of the S antigen (whether wild type or mutated as disclosed herein) that enables effective presentation of the epitopes, especially of the B-epitopes, to the immune system of the host.
  • the experimental data disclosed herein show that an administration route encompassing a step of administration to upper respiratory tract of the host may improve the immune response in some tissues or organs targeted by the virus. These results are surprising and unexpected.
  • the data in the examples also demonstrate: (i) strong CD8 + T-cell responses induced by NILV::S CoV-2 Wuhan at the systemic level, (ii) notable proportions of IFN- ⁇ - producing lung CD8+ T cells, specific to several S CoV-2 epitopes, (iii) high proportions of lung CD8 + T cells with effector memory (Tem) and resident memory (Trm) phenotye, (iv) recruitment of CD8 + T cells in the olfactory bulbs, detectable in mice vaccinated and challenged with SARS-CoV-2 Wuhan or SARS-CoV-2 P.1 variant.
  • this invention provides a method of inducing a protective immune response against Severe Acute Respiratory Syndrome beta- coronavirus 2 (SARS-CoV-2) in a subject, comprising administering to the upper respiratory tract of the subject an effective amount of an agent that induces a protective immune response against SARS-CoV-2.
  • the agent that induces a protective immune response against SARS-CoV-2 is a pseudotyped LV vector particle encoding a SARS-CoV-2 Spike (S) glycoprotein or a derivative or fragment thereof.
  • the agent is administered by aerosol inhalation. In some embodiments the agent is administered by nasal instillation. In some embodiments the agent is administered by nasal insufflation. In some embodiments the treatment course consists of a single administration to the upper respiratory tract. In some embodiments the treatment course comprises at least one priming administration outside the respiratory tract followed by at least one boosting administration to the upper respiratory tract.
  • the protective immune response comprises production of SARS- CoV-2 neutralizing antibodies in the subject. In some embodiments the neutralizing antibodies comprise IgG antibodies. In some embodiments the neutralizing antibodies comprise IgA antibodies. In some embodiments the protective immune response comprises production of SARS-CoV-2 S-specific T cells in the subject.
  • the SARS-CoV-2 S-specific T cells comprise CD4 + T cells, CD8 + T cells, or both CD4+ and CD8+ T cells. In some embodiments the SARS-CoV-2 S-specific T cells comprise lung CD8+ T cells. In some embodiments the SARS-CoV-2 S-specific T cells comprise IFN- ⁇ -producing T-cells. In some embodiments the CD8+ T cells comprise T cells with an effector memory (Tem) and/or resident memory (Trm) phenotype. In some embodiments the SARS-CoV-2 S-specific T cells are recruited to the olfactory bulb. In some embodiments the protective immune response provides a reduced likelihood of developing SARS-CoV-2 infection-related inflammation in the subject.
  • the SARS-CoV-2 S protein derivative has an amino acid sequence at least 95% identical to SEQ ID NO: 1. In some embodiments the SARS-CoV-2 S protein derivative is expressed from a coding sequence having a nucleotide sequence at least 80% identical to SEQ ID NO: 2. In some embodiments the SARS-CoV-2 S protein fragment comprises a peptide selected from peptide 61-75 (NVTWFHAIHVSGTNG (SEQ ID NO: 15)), peptide 536-550 (NKCVNFNFNGLTGTG (SEQ ID NO: 16)) and peptide 576- 590 (VRDPQTLEILDITPC (SEQ ID NO: 17)).
  • the SARS-CoV-2 S derivative or fragment thereof comprises an amino acid modification relative to SEQ ID NO: 1, the modification selected from: (i) 986K ⁇ P and 987V ⁇ P, (ii) 681PRRARS686 (SEQ ID NO: 22) ⁇ 681 PGSAGS 686 (SEQ ID NO: 23), and (iii) 986 K ⁇ P, 987V ⁇ P , and 675QTQTNSPRRAR685 (SEQ ID NO: 24) deletion.
  • the Severe Acute Respiratory Syndrome beta-coronavirus 2 (SARS-CoV-2) spike (S) protein or a derivative or fragment thereof comprises or consists of an amino acid sequence selected from SEQ ID NOS: 1, 5, 8, 11, 14, 108, 111, 114, 117, and 120.
  • the SARS-CoV-2 S protein or a derivative or fragment thereof comprises of SEQ ID NO: 1.
  • the SARS-CoV-2 S protein or a derivative or fragment thereof consists of SEQ ID NO: 1.
  • the SARS-CoV-2 S protein or a derivative or fragment thereof comprises of SEQ ID NO: 5.
  • the SARS-CoV-2 S protein or a derivative or fragment thereof consists of SEQ ID NO: 5. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof comprises of SEQ ID NO: 8. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof consists of SEQ ID NO: 8. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof comprises of SEQ ID NO: 11. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof consists of SEQ ID NO: 11. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof comprises of SEQ ID NO: 14.
  • the SARS-CoV-2 S protein or a derivative or fragment thereof consists of SEQ ID NO: 14. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof comprises of SEQ ID NO: 108. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof consists of SEQ ID NO: 108. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof comprises of SEQ ID NO: 111. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof consists of SEQ ID NO: 111. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof comprises of SEQ ID NO: 114.
  • the SARS-CoV-2 S protein or a derivative or fragment thereof consists of SEQ ID NO: 114. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof comprises of SEQ ID NO: 117. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof consists of SEQ ID NO: 117. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof comprises of SEQ ID NO: 120. In some embodiments the SARS-CoV-2 S protein or a derivative or fragment thereof consists of SEQ ID NO: 120. In some embodiments the administered LV vector particle is integrative (ILV).
  • ILV integrative
  • the administered lentiviral vector particle is nonintegrative with a defective integrase protein (NILV).
  • NILV defective integrase protein
  • the administered NILV comprises a D64V mutation in an integrase coding sequence.
  • the administered LV vector particle is pseudotyped with Vesicular Stomatitis Virus envelop Glycoprotein (VSV-G).
  • VSV-G Vesicular Stomatitis Virus envelop Glycoprotein
  • the LV vector particle is administered as a vaccine formulation comprising the LV vector particle and a pharmaceutically acceptable carrier.
  • the invention relates to a dosage form for administration to the upper respiratory tract of a subject of a pseudotyped LV vector particle encoding a SARS- CoV-2 Spike (S) protein or a derivative or fragment thereof.
  • S SARS- CoV-2 Spike
  • the dosage form is for administration by aerosol inhalation. In some embodiments the dosage form is for administration by nasal instillation. In some embodiments the dosage form is for administration by nasal insufflation.
  • the SARS-CoV-2 S protein derivative has an amino acid sequence at least 95% identical to SEQ ID NO: 1. In some embodiments the SARS-CoV-2 S protein derivative is expressed from a coding sequence having a nucleotide sequence at least 80% identical to SEQ ID NO: 2.
  • the SARS-CoV-2 S protein fragment comprises a peptide selected from peptide 61-75 (NVTWFHAIHVSGTNG (SEQ ID NO: 15)), peptide 536-550 (NKCVNFNFNGLTGTG (SEQ ID NO: 16)) and peptide 576-590 (VRDPQTLEILDITPC (SEQ ID NO: 17)).
  • the SARS-CoV-2 S derivative or fragment thereof comprises an amino acid modification relative to SEQ ID NO: 1, the modification selected from: (i) 986 K ⁇ P and 987 V ⁇ P , (ii) 681 PRRARS 686 (SEQ ID NO: 22) ⁇ 681 PGSAGS 686 (SEQ ID NO: 23), and (iii) 986K ⁇ P, 987V ⁇ P, and 675QTQTNSPRRAR685 (SEQ ID NO: 24) deletion. Additional derivatives and fragments of the S protein are disclosed below along with various aspects of the invention.
  • the administered LV vector particle is integrative (ILV).
  • the administered LV vector particle is nonintegrative (NILV).
  • the NILV particle comprises a D64V mutation in an integrase coding sequence.
  • the lentiviral vector particle is pseudotyped with Vesicular Stomatitis Virus envelop Glycoprotein (VSV-G).
  • VSV-G Vesicular Stomatitis Virus envelop Glycoprotein
  • a kit is provided. The kit may be suitable for use in practicing a method disclosed herein.
  • the kit comprises a dosage form for administration to the upper respiratory tract of a subject of the pseudotyped LV vector particle encoding a SARS-CoV-2 S protein or a derivative or fragment thereof according to this disclosure.
  • the applicator for administration is an applicator for aerosol inhalation.
  • the applicator for administration to the upper respiratory tract of a subject is an applicator for nasal instillation. In some embodiments the applicator for administration to the upper respiratory tract of a subject is an applicator for nasal insufflation.
  • novel and nonobvious pseudotyped LV vector particles encoding a SARS-CoV-2 Spike (S) protein or a derivative or fragment thereof.
  • the pseudotyped LV vector particles are administered to the upper respiratory tract of a subject.
  • the pseudotyped LV vector particles induce a protective immune response providing a reduced likelihood of developing SARS- CoV-2 infection-related inflammation following administration to the upper respiratory tract of a subject.
  • the SARS-CoV-2 S protein derivative has an amino acid sequence at least 95% identical to SEQ ID NO: 1. In some embodiments the SARS-CoV-2 S protein derivative is expressed from a coding sequence having a nucleotide sequence at least 80% identical to SEQ ID NO: 2. In some embodiments the SARS-CoV-2 S protein fragment comprises a peptide selected from Peptide 61-75 (NVTWFHAIHVSGTNG – SEQ ID No.15 ), peptide 536-550 (NKCVNFNFNGLTGTG– SEQ ID No.16) and peptide 576-590 (VRDPQTLEILDITPC– SEQ ID No.17).
  • the SARS-CoV-2 S derivative or fragment thereof comprises an amino acid modification relative to SEQ ID NO: 1, the modification selected from: (i) 986K ⁇ P and 987 V ⁇ P , (ii) 681 PRRARS 686 (SEQ ID NO: 22) ⁇ 681 PGSAGS 686 (SEQ ID NO: 23), and (iii) 986 K ⁇ P, 987V ⁇ P , and 675QTQTNSPRRAR685 (SEQ ID NO: 24) deletion.
  • the LV vector particle is integrative (ILV).
  • the lentiviral vector particle is nonintegrative (NILV).
  • the NILV particle comprises a D64V mutation in an integrase coding sequence.
  • the LV vector particle is pseudotyped with Vesicular Stomatitis Virus envelop Glycoprotein (VSV-G).
  • the pseudotyped LV vector particle encodes a Spike glycoprotein, or fragment or derivative thereof, that has the same amino acid sequence as the spike protein, or fragment or derivative thereof, that is encoded by vector selected from: pFlap-ieCMV-S2P ⁇ F-WPREm (also named pFlap-ieCMV-S2PdeltaF-WPREm) (CNCM I-5537), pFlap-ieCMV-S2P3F-WPREm (CNCM I-5538), pFlap-ieCMV-S2P- WPREm (CNCM I-5539), pFlap-ieCMV-SFL-WPREm (CNCM I-5540), pFlap-ieCMV-S- B1.1.7-WPREm (CNCM I-5708), pFlap-ieCMV-S-B351-WPREm (CNCM I-5709), pFlap- ieCMV-S
  • a host cell comprising a vector selected from: pFlap-ieCMV- S2P ⁇ F-WPREm (CNCM I-5537), pFlap-ieCMV-S2P3F-WPREm (CNCM I-5538), pFlap- ieCMV-S2P-WPREm (CNCM I-5539), pFlap-ieCMV-SFL-WPREm (CNCM I-5540), pFlap-ieCMV-S-B1.1.7-WPREm (CNCM I-5708), pFlap-ieCMV-S-B351-WPREm (CNCM I-5709), pFlap-ieCMV-S-B351-2P-WPREm (CNCM I-5710), pFlap-ieCMV-SFL- D614G-WPREm (CNCM I-5711), pFlap-ieCMV-S-P1-WP
  • the vector is stably integrated into the host cell genome, while in other embodiments it is not.
  • a pseudotyped LV vector particle encoding a SARS-CoV-2 Spike (S) glycoprotein or a derivative or fragment thereof, wherein the pseudotyped LV vector particle is made by a method comprising co-transfection of a host cell with a vector selected from: pFlap-ieCMV-S2P ⁇ F-WPREm (CNCM I-5537), pFlap-ieCMV-S2P3F- WPREm (CNCM I-5538), pFlap-ieCMV-S2P-WPREm (CNCM I-5539), pFlap-ieCMV- SFL-WPREm (CNCM I-5540), pFlap-ieCMV-S-B1.1.7-WPREm (CNCM I-5708), pFlap- ieCMV-S-B351-WPREm (
  • ⁇ Figure 3 Set up of a murine model expressing hACE2 in the respiratory tracts.
  • A Detection of hACE2 expression by RT-PCR in HEK293 T cells transduced with Ad5::hACE2, at 2 days post transduction. NT: Not transduced.
  • C GFP expression in lung cells prepared at day 4 after i.n.
  • Lung hematopoietic CD45 + cells were analyzed by use of antibodies specific to surface markers, or combination of surface markers, allowing characterization of innate immune cell populations, via 3 distinct paths and by sequential gating. The cell populations are highlighted in grey.
  • B Percentages of each innate immune subset versus total lung CD45 + cells at 3 dpi in mice sham-vaccinated or vaccinated with LV::SFL, following various prime-boost regimen compared to non-infected (NI) controls which only received PBS. All mice were pretreated with Ad5::hACE-2, 4 days prior to SARS-CoV-2 inoculation.
  • A Timeline of the LV::S FL prime-boost/target immunization regimen and SARS-CoV-2 challenge in hamsters. Sham-vaccinated received an empty LV.
  • B Dynamic of anti-S CoV-2 Ab response following LV immunization. Sera were collected from sham- or LV-vaccinated hamsters at 3, 5 (pre-boost), and 6 (post-boost) weeks after the prime injection. Anti-S CoV-2 IgG responses were evaluated by ELISA and expressed as mean endpoint dilution titers.
  • C Post boost/target EC50 neutralizing titers, determined in the hamsters’ sera after boost, and as compared to the sera from a cohort of asymptomatic (AS), pauci-symptomatic (PS), symptomatic COVID-19 cases (S) or hospitalized (H) humans.
  • D Weight follow-up in hamsters, either sham- or LV::S FL - vaccinated with diverse regimens. For further clarity, only the individuals reaching 4 dpi are shown. Those sacrificed at 2 dpi had the same mean weight as their counterparts of the same groups between 0 and 2 dpi.
  • LV::S FL vaccination reduces SARS-Co-2-mediated histopathology in golden hamsters. Animals are those detailed in the Figure 6.
  • A Determination of log 2 fold change in cytokines and chemokines mRNA expression in mice sham-vaccinated or vaccinated with LV::S FL , following various prime-boost regimen. The same order of appearance for each construct and regimen applies in each determination.
  • B Histological analysis HE&S lung shown for 2 and 4 dpi. Original magnification: x10, scale bar: 100 ⁇ m.
  • C Neutralization capacity of anti-S CoV-2 Abs, expressed as EC50 neutralizing titers, determined in the sera and lung homogenates of LV::S ⁇ F2P -immunized hamsters.
  • D Percentages of weight loss in LV::S ⁇ F2P - or sham- vaccinated hamsters at 4 dpi.
  • C-D Cytometric analysis at 3 dpi performed on cells extracted from pooled olfactory bulbs or brain of LV::S ⁇ F2P i.m.- i.n. vaccinated and protected mice versus sham-vaccinated and unprotected mice.
  • C Adaptive and
  • D innate immune cells in the olfactory bulbs.
  • E Innate immune cells in the brain.
  • Figure 17 Maps of lentiviral plasmid encoding S FL ,S1-S2, S1, S 2P, S 2P3F S ⁇ F2P
  • Figure 18 Head to head comparison of the protective potential of ILV::S FL or ILV::S ⁇ F2P in C57BL/6 mice pre-treated with Ad5::hACE2 and challenged with SARS- CoV-2.C57BL/6 mice were primed i.m. and boosted i.n. as described in Example 1. The animals were challenged i.n. with SARS-CoV-2 and viral load was measured at 3 dpi.
  • Figure 19 plasmid map for pFLAP K18-hACE2 WPRE
  • Figures 20 to 24 Sequences of pFlap-CMV-S-2019-nCoV-WPREm, pFlap- ieCMV-S2P-WPREm, pFlap-ieCMV-S2P3F-WPREm, pFlap-ieCMV-S2P- ⁇ F-WPREm, pFLAP K18-hACE2 WPRE and the transgene sequences.
  • Figure 25 plasmid map for pFLAP K18-hACE2 WPRE
  • NILV::S CoV-2 Full protective capacity of NILV::S CoV-2 against the Manaus P.1 SARS- CoV-2 variant.
  • B Brain or lung viral RNA contents, determined by conventional E-specific or sub-genomic Esg-specific qRT-PCR at 3dpi.
  • mice out of the 5 sham- vaccinated mice did not have detectable viral load in the lungs despite a high viral in the brain and hACE2 mRNA expression level comparable to the other mice in the same group.
  • C Neutralizing activity (EC50) of sera from individual NILV::S CoV-2- vaccinated mice against pseudo-viruses harboring S CoV-2 from the ancestral Wuhan strain or D614G, B1.117, B1.351 or P.1 variants.
  • T-cell response plays a major role in NILV::S CoV-2 -mediated protection against SARS-CoV-2.
  • A-B CD3 immuno-histo-chemistry of an olfactory bulb from a NILV::S CoV-2 i.m.-i.n. vaccinated and protected mice or unprotected sham-vaccinated mice and representative results from these groups at 3dpi with SARS-CoV-2 Wuhan.
  • C Cytometric analysis of cells extracted from pooled olfactory bulbs from the same groups.
  • D-E density of CD3 T cells as determined by immuno-histo-chemistry of an olfactory bulb from a NILV::S CoV-2 i.m.-i.n.
  • (A) Timeline of i.p.-i.p. immunization in C57BL/6 mice (n 5/group).
  • Figures 30-34 Sequences of pFlap-ieCMV-S-B1.1.7-WPREm, pFlap-ieCMV-S- B351-WPREm, pFlap-ieCMV-S-B351-2P-WPREm, pFlap-ieCMV-SFL-D614G-WPREm, pFlap-ieCMV-S-P1-WPREm and the transgene sequences.
  • the sequences disclosed herein that are related to the transgene constructs are specified by their SEQ ID No. as follows: DETAILED DESCRIPTION
  • the inventions described herein are based in part on the potent vaccination strategy demonstrated in the examples.
  • the examples demonstrate the utility of the the etiologic agent of CoronaVirus Disease 2019 (COVID-19).
  • LV::S FL full-length, membrane anchored S
  • mutated prefusion an optionally stabilized form
  • LV::S ⁇ F2P also designated LV::S2P ⁇ F or LV::S2PDF or LV::S2PdeltaF
  • hACE2 human Angiotensin-Converting Enzyme 2
  • S-specific T cells were also abundantly induced in LV::S FL - or LV::S ⁇ F2P -vaccinated individuals.
  • mice in which the expression of hACE2 was induced by transduction of the respiratory tract cells by an adenoviral type 5 (Ad5) vector or by transgenesis with hACE2 vectorized by LV vector (B6.K18-hACE2IP- THV mice), as well as in hamsters, substantial or full protective effect against pulmonary SARS-CoV-2 replication was afforded when LV::S FL or LV::S ⁇ F2P was used in systemic prime immunization, followed by intranasal mucosal boost/target. The conferred protection avoided pulmonary inflammation and prevented tissue damage.
  • SARS-CoV-2 S Protein comprises the following amino acid sequence (Genbank: YP_009724390.1; SEQ ID NO: 1): 241 LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK 301 CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN 361 CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIAD 421 YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC 481 NGVEGFNCYF PLQSYGFQ
  • the definitions provided herein for the SARS-CoV-2 S protein or the polynucleotide encoding the SARS-CoV-2 S protein similarly apply to the derivatives or to the fragments of the SARS-CoV-2 S protein defined with respect to the sequences of SEQ ID No.1 or respectively SEQ ID No.2.
  • the SARS-CoV-2 S protein comprises an amino acid sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 1.
  • SARS-CoV-2 S protein may qualify as a SARS-CoV-2 S protein derivative and/or as a SARS-CoV-2 S protein fragment if the obtained sequence is shorter than SEQ ID NO: 1. It may also be a sequence of a SARS-CoV-2 S protein expressed by a different strain of the virus than the originally identified isolate Wuhan-Hu- 1 (accession number MN908947). In some embodiments the SARS-CoV-2 S protein consists of an amino acid sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 1.
  • SARS-CoV-2 S protein may qualify as a SARS-CoV-2 S protein derivative and/or as a SARS-CoV-2 S protein fragment if the obtained sequence is shorter than SEQ ID NO: 1. It may also be a sequence of a SARS-CoV-2 S protein expressed by a different strain of the virus than the originally identified isolate Wuhan-Hu- 1 (accession number MN908947).
  • the SARS-CoV-2 S protein derivative has an amino acid sequence at least 95% identical or at least 99% identical to SEQ ID NO:1.
  • the SARS-CoV-2 spike protein derivative or fragment has the amino acid sequence of SEQ ID No.8, SEQ ID No.11, SEQ ID No.108, SEQ ID No.
  • SARS-CoV-2 S protein derivative has an amino acid sequence at least 95% identical or at least 99% identical to S SEQ ID No.8, SEQ ID No.11, SEQ ID No.108, SEQ ID No.111, SEQ ID No.114, SEQ ID No.117, or SEQ ID No.120or the SARS-CoV-2 spike protein fragment has the amino acid sequence of SEQ ID No.14 or the SARS-CoV-2 S protein derivative has an amino acid sequence at least 95% identical or at least 99% identical to SEQ ID NO: 14.
  • the SARS-CoV-2 S protein comprises an amino acid sequence that has 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid changes relative to SEQ ID NO: 1. In some embodiments the SARS-CoV-2 S protein comprises of an amino acid sequence that has no more than 1, no more than 2, no more than 3, no more than 4, no more than 5, no more than 6, no more than 7, no more than 8, no more than 9 or no more than 10 amino acid changes relative to SEQ ID NO: 1.
  • Such SARS-CoV-2 S protein may qualify as a SARS-CoV-2 S protein derivative and/or as a SARS-CoV-2 S protein fragment if the obtained sequence is shorter than SEQ ID NO: 1.
  • SARS-CoV-2 S protein may also be a sequence of a SARS-CoV-2 S protein expressed by a different variant of the virus than the originally identified isolate Wuhan-Hu-1 (accession number MN908947).
  • the SARS-CoV-2 S protein consists of an amino acid sequence that has 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid changes relative to SEQ ID NO: 1.
  • the SARS-CoV-2 S protein consist of an amino acid sequence that has no more than 1, no more than 2, no more than 3, no more than 4, no more than 5, no more than 6, no more than 7, no more than 8, no more than 9 or no more than 10 amino acid changes relative to SEQ ID NO: 1 in particular no more than 10 amino acid changes at a single location in the protein.
  • the SARS-CoV-2 S protein harbors mutation(s) such as those of the nucleotide sequence encoding S2PAF or S2P3F
  • a SARS-CoV-2 Spike protein comprises mutation(s) in the Receptor Binding Domain of the protein.
  • the SARS-CoV-2 Spike protein harbors a substitution at residue 614 such as D614G or comprises such substitution.
  • the SARS-CoV-2 Spike protein harbors mutation(s) identified in so-called variant SARS-CoV-2 VUI 2020 12/01 S protein i.e.
  • mutations by substitution or deletion of amino acid residues of the Spike protein such as deletion 69- 70, deletion 144, N501Y, substitutions A570D, D614G, P681 H, T716I, S982A and D1118H.
  • the SARS-CoV-2 Spike protein harbors mutation(s) that are present in SEQ ID No. 108, SEQ ID No. 111 , SEQ ID No. 114, SEQ ID No. 117, or SEQ ID No. 120.
  • the SARS-CoV-2 S protein is encoded by a nucleotide sequence that comprises nucleotides 21563 to 25384 of Genbank: NC_045512.2 (SEQ ID NO: 2): In a preferred embodiment the SARS-CoV-2 S protein is encoded by a nucleotide sequence that consists of nucleotides 21563 to 25384 of Genbank: NC_045512.2 (SEQ ID NO: 2).
  • the SARS-CoV-2 S protein is encoded by a nucleotide sequence that is at least 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 2.
  • SARS-CoV-2 S protein may qualify as a SARS-CoV-2 S protein derivative and/or as a SARS-CoV-2 S protein fragment if the nucleotide sequence having such defined percentage of identity is shorter than SEQ ID NO: 2. It may also be a sequence encoding a SARS-CoV-2 S protein which originates from a different strain of the virus than the originally identified isolate Wuhan-Hu-1 (accession number MN908947).
  • the nucleotide sequence encoding the SARS-CoV-2 Spike protein harbors mutation(s) encompassing at least one non-synonymous mutation.
  • the SARS-CoV-2 S protein is encoded by a nucleotide sequence that harbors mutation(s) such as those of the nucleotide sequence encoding S2P ⁇ F or S2P3F.
  • the nucleotide sequence encoding the SARS-CoV-2 Spike protein harbors a mutation at location 23403 in the sequence of SEQ ID No.2 wherein codon GGT is mutated, in particular substituted for codon GAT (corresponding to mutation at location 614, in particular to D614G substitution in the encoded protein).
  • the nucleotide sequence is the sequence encoding the Spike protein of the so-called variant SARS-CoV-2 VUI 202012/01 wherein the Spike protein harbors multiple mutations by substitution or deletion of nucleotides wherein the mutations lead to the following changes in the amino acid residues of the encoded Spike protein: deletion 69-70, deletion 144, substitutions N501Y, A570D, D614G, P681H, T716I, S982A and D1118H.
  • the SARS-CoV-2 S protein is encoded by a nucleotide sequence that is codon-optimized, such as a codon optimized variant of SEQ ID NO: 2.
  • the SARS-CoV-2 S protein comprises K986P and V987P amino acid substitutions.
  • the SARS-CoV-2 S protein comprises a modification in which amino acids 681-686 are changed PRRARS (SEQ ID NO: 22) to PGSAGS (SEQ ID NO: 23).
  • the SARS-CoV-2 S protein comprises a modification in which amino acids 675-685 (QTQTNSPRRAR (SEQ ID NO: 24)) are deleted.
  • a “lentiviral vector” means a non-replicating vector for the transduction of a host cell with a transgene comprising c/s- acting lentiviral RNA or DNA sequences, and requiring lentiviral proteins (e.g., Gag, Pol, and/or Env) that are provided in trans.
  • the lentiviral vector lacks expression of functional Gag, Pol, and Env proteins.
  • the lentiviral vector may be present in the form of an RNA or DNA molecule, depending on the stage of production or development of said retroviral vectors.
  • the lentiviral vector can be in the form of a recombinant DNA molecule, such as a plasmid.
  • the lentiviral vector can be in the form of a lentiviral vector particle, such as an RNA molecule(s) within a complex of lentiviral other proteins.
  • lentiviral particle vectors which correspond to modified or recombinant lentivirus particles, comprise a genome which is composed of two copies of single-stranded RNA. These RNA sequences can be obtained by transcription from a double-stranded DNA sequence inserted into a host cell genome (proviral vector DNA) or can be obtained from the transient expression of plasmid DNA (plasmid vector DNA) in a transformed host cell.
  • the lentiviral vector particles may have the capacity for integration. As such, they contain a functional integrase protein. Alternatively, the lentiviral vector particles may have impaired or no capacity for integration. Non-integrating vector particles have one or more mutations that eliminate most or all of the integrating capacity of the lentiviral vector particles. For, example, a non-integrating vector particle can contain mutation(s) in the integrase encoded by the lentiviral pol gene that cause a reduction in integrating capacity. In contrast, an integrating vector particle comprises a functional integrase protein that does not contain any mutations that eliminate most or all of the integrating capacity of the lentiviral vector particles.
  • the lentiviral vector particles are integrative (ILV).
  • the lentiviral vector particles are non-integrative (NILV).
  • ⁇ Lentiviral vectors derive from lentiviruses, in particular human immunodeficiency virus (HIV-1 or HIV-2), simian immunodeficiency virus (SIV), equine infectious encephalitis virus (EIAV), caprine arthritis encephalitis virus (CAEV), bovine immunodeficiency virus (BIV) and feline immunodeficiency virus (FIV), which are modified to remove genetic determinants involved in pathogenicity and introduce new determinants useful for obtaining therapeutic effects.
  • lentiviral vectors derive from HIV-1.
  • ⁇ Such vectors are based on the separation of the cis- and trans- acting sequences.
  • the trans-acting sequences e.g., gag, pol, tat, rev, and env genes
  • the trans-acting sequences can be deleted and replaced by an expression cassette encoding a transgene.
  • ⁇ Efficient integration and replication in non-dividing cells generally requires the presence of two cis- acting sequences at the center of the lentiviral genome, the central polypurine tract (cPPT) and the central termination sequence (CTS). These lead to the formation of a triple-stranded DNA structure called the central DNA “flap”, which acts as a signal for uncoating of the pre-integration complex at the nuclear pore and efficient importation of the expression cassette into the nucleus of non-dividing cells, such as dendritic cells.
  • cPPT central polypurine tract
  • CTS central termination sequence
  • the invention encompasses a lentiviral vector comprising a central polypurine tract and central termination sequence referred to as cPPT/CTS sequence as described, in particular, in the European patent application EP 2 169 073.
  • ⁇ Further sequences are usually present in cis, such as the long terminal repeats (LTRs) that are involved in integration of the vector proviral DNA sequence into a host cell genome.
  • LTRs long terminal repeats
  • Vectors may be obtained by mutating the LTR sequences, for instance, in domain U3 of said LTR (DII3) (Miyoshi H et al, 1998, J Virol. 72(10):8150-7; Zufferey et a!., 1998, J Virol 72(12):9873-80).
  • the vector does not contain an enhancer.
  • the lentiviral vector comprises LTR sequences, preferably with a mutated U3 region ( ⁇ U3) removing promoter and enhancer sequences in the 3’ LTR.
  • the packaging sequence ⁇ (psi) can also be incorporated to help the encapsidation of the polynucleotide sequence into the vector particles (Kessler et al., 2007, Leukemia, 21(9):1859-74; Paschen et al., 2004, Cancer Immunol Immunother 12(6):196-203).
  • the invention encompasses a lentiviral vector comprising a lentiviral packaging sequence ⁇ (psi).
  • the lentiviral vector comprises a PBS.
  • the invention encompasses a lentiviral vector comprising a WPRE and/or an IRES.
  • the lentiviral vector comprises at least one cPPT/CTS sequence, one ⁇ sequence, one (preferably 2) LTR sequence, and an expression cassette including a transgene under the transcriptional control of a cytomegalovirus (CMV) immediate-early promoter, a ⁇ 2m promoter or a class I MHC promoter.
  • CMV cytomegalovirus
  • Methods of producing lentiviral vector particles and lentiviral vector particles are also provided.
  • a lentiviral vector particle (or lentiviral particle vector) comprises a lentiviral vector in association with viral proteins.
  • the vector may be an integrating vector (IL) (in particular for the preparation of transgenic mice as illustrated below) or may be a non- integrating vector (NIL) in particular for administration to human subject.
  • IL integrating vector
  • NIL non- integrating vector
  • the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof according to any of the embodiments disclosed herein. In some embodiments, the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises or consists of an amino acid sequence selected from SEQ ID NOS: 1, 5, 8, 11, 14, 108, 111, 114, 117, and 120. In some embodiments, the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises or consists of the amino acid sequence of SEQ ID NO: 1.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises or consists of the amino acid sequence of SEQ ID NO: 5. In some embodiments, the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises or consists of the amino acid sequence of SEQ ID NO: 8. In some embodiments, the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises or consists of the amino acid sequence of SEQ ID NO: 11. In some embodiments, the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises or consists of the amino acid sequence of SEQ ID NO: 14.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises or consists of the amino acid sequence of SEQ ID NO: 108. In some embodiments, the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises or consists of the amino acid sequence of SEQ ID NO: 111. In some embodiments, the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises or consists of the amino acid sequence of SEQ ID NO: 114.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises or consists of the amino acid sequence of SEQ ID NO: 117. In some embodiments, the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises or consists of the amino acid sequence of SEQ ID NO: 120. In some embodiments, the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that consists of the amino acid sequence Genbank: YP_009724390.1 (SEQ ID NO: 1).
  • the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises an amino acid sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 1.
  • SEQ ID NO: 1 The specific embodiments of such protein S derivative or fragment are also encompassed within these embodiments of the lentiviral vector particles.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises an amino acid sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NOS: 5, 8, 11, 14, 108, 111, 114, 117, or 120.
  • SEQ ID NOS: 5, 8, 11, 14, 108, 111, 114, 117, or 120 The specific embodiments of such protein S derivative or fragment are also encompassed within these embodiments of the lentiviral vector particles.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that consists of an amino acid sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 1.
  • SARS-CoV-2 S protein or a derivative or fragment thereof that consists of an amino acid sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 1.
  • the specific embodiments of such protein S derivative or fragment disclosed herein are also encompassed within these embodiments of the lentiviral vector particles.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that consists of an amino acid sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NOS: 5, 8, 11, 14, 108, 111, 114, 117, or 120.
  • the specific embodiments of such protein S derivative or fragment are also encompassed within these embodiments of the lentiviral vector particles.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises an amino acid sequence that has 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid changes relative to SEQ ID NO: 1.
  • the SARS-CoV-2 S protein comprises of an amino acid sequence that has no more than 1, no more than 2, no more than 3, no more than 4, no more than 5, no more than 6, no more than 7, no more than 8, no more than 9 or no more than 10 amino acid changes relative to SEQ ID NO: 1.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that comprises an amino acid sequence that has 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid changes relative to SEQ ID NOS: 5, 8, 11, 14, 108, 111, 114, 117, or 120.
  • the SARS-CoV-2 S protein comprises of an amino acid sequence that has no more than 1, no more than 2, no more than 3, no more than 4, no more than 5, no more than 6, no more than 7, no more than 8, no more than 9 or no more than 10 amino acid changes relative to SEQ ID NO: 1.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that consists of an amino acid sequence that has 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid changes relative to SEQ ID NO: 1.
  • the SARS-CoV-2 S protein consists of an amino acid sequence that has no more than 1, no more than 2, no more than 3, no more than 4, no more than 5, no more than 6, no more than 7, no more than 8, no more than 9 or no more than 10 amino acid changes relative to SEQ ID NO: 1.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein or a derivative or fragment thereof that consists of an amino acid sequence that has 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid changes relative to SEQ ID NOS: 5, 8, 11, 14, 108, 111, 114, 117, or 120.
  • the SARS-CoV-2 S protein consists of an amino acid sequence that has no more than 1, no more than 2, no more than 3, no more than 4, no more than 5, no more than 6, no more than 7, no more than 8, no more than 9 or no more than 10 amino acid changes relative to SEQ ID NO: 1.
  • the lentiviral vector particles encode a SARS-CoV-2 Spike protein that harbors mutation(s) such as those contained in S2P ⁇ F (S2PdeltaF) or S2P3F protein derivatives.
  • the lentiviral vector particles encode a SARS-CoV-2 Spike protein that harbors a substitution at residue 614 such as D614G or that comprises such substitution.
  • the lentiviral vector particles encode a SARS-CoV-2 Spike protein that harbors mutation(s) identified in so-called variant SARS-CoV-2 VUI 202012/01 S protein i.e., mutations by substitution or deletion of amino acid residues of the Spike protein such as deletion 69-70, deletion 144, N501Y, substitutions A570D, D614G, P681H, T716I, S982A and D1118H.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein that is encoded by a nucleotide sequence that comprises SEQ ID NO: 2.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein that is encoded by a nucleotide sequence that consists of nucleotides 21563 to 25384 of Genbank: NC_045512.2 (SEQ ID NO: 2).
  • the lentiviral vector particles comprise a nucleotide sequence that is at least 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 2.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein that is encoded by the nucleotide sequence that harbors mutation(s) with respect to the sequence of SEQ ID NO: 2, wherein the mutation(s) encompass at least one non- synonymous mutation.
  • the lentiviral vector particles encode a SARS-CoV-2 S protein whose nucleotide sequence harbors a mutation at location 23403 in the sequence of SEQ ID No.2 wherein codon GGT is mutated, in particular substituted for codon GAT (corresponding to mutation at location 614, in particular to D614G substitution in the encoded S protein of SEQ ID No.1).
  • the lentiviral vector particles encode the Spike protein of the so-called variant SARS-CoV-2 VUI 2020 12/01 wherein the Spike protein harbors multiple mutations by substitution or deletion of nucleotides with respect to the sequence of SEQ ID No.2 and wherein the nucleotide mutations lead to the following changes in the amino acid residues of the encoded Spike protein: deletion 69-70, deletion 144, substitutions N501Y, A570D, D614G, P681H, T716I, S982A and D1118H.
  • the lentiviral vector particles comprise a nucleotide sequence that is codon-optimized, such as a codon optimized variant of SEQ ID NO: 2 or a codon optimized variant of the nucleotide sequence encoding the S2P ⁇ F (S2PdeltaF) or the S2P3F derivatives.
  • the lentiviral vector particles comprise a nucleotide sequence that encodes a SARS-CoV-2 S protein that comprises K986P and V987P amino acid substitutions.
  • the lentiviral vector particles comprise a nucleotide sequence that encodes a SARS-CoV-2 S protein that comprises a modification in which amino acids 681-686 PRRARS (SEQ ID No.22) are changed to PGSAGS (SEQ ID No.23) such as in LV::S2P3F.
  • the lentiviral vector particles comprise a nucleotide sequence that encodes a SARS-CoV-2 S protein that comprises a modification in which amino acids 675-685 (QTQTNSPRRAR) (SEQ ID No.24) are deleted such as in LV::S2P ⁇ F (LV::S2PdeltaF).
  • the pseudotyped lentiviral vector particles comprise a polynucleotide selected from: - a polynucleotide encoding S2P ⁇ F (S2PdeltaF) of SEQ ID No. 13 or a coding sequence having a nucleotide sequence at least 80% identical to SEQ ID No.13, in particular a coding sequence having a mutation, in particular a deletion, in the RBD, - a polynucleotide encoding S2P3F of SEQ ID No.10 or a coding sequence having a nucleotide sequence at least 80% identical to SEQ ID No.10 having a mutation in the RBD, in particular wherein the coding sequence having a nucleotide sequence at least 80% identical to SEQ ID No.10 comprises mutations 986 K ⁇ P and 987 V ⁇ P.
  • the lentiviral vector particle comprises HIV-1 Gag and Pol proteins.
  • the lentiviral vector particle comprises subtype D, especially HIV-1 NDK , Gag and Pol proteins.
  • the lentivector particles are obtained in a host cell transformed with a DNA plasmid.
  • a DNA plasmid can comprise: - bacterial origin of replication (ex: pUC ori); - antibiotic resistance gene (ex: KanR) for selection; and more particularly: - a lentiviral vector comprising at least one nucleic acid encoding a SARS-CoV-2 S protein or a derivative or fragment thereof, transcriptionally linked to a CMV promoter.
  • Such a method allows producing a recombinant vector particle according to the invention, comprising the following steps of: i) transfecting a suitable host cell with a lentiviral vector; ii) transfecting said host cell with a packaging plasmid vector, containing viral DNA sequences encoding at least structural and polymerase (+ integrase) activities of a retrovirus (preferably lentivirus);
  • packaging plasmids are described in the art (Dull et al., 1998, J Virol, 72(11):8463-71; Zufferey et al., 1998, J Virol 72(12):9873-80).
  • pseudotyping extends the spectrum of cell types that may be transduced while avoiding being the target of pre-existing immunity in human populations.
  • the host cell can be further transfected with one or several envelope DNA plasmid(s) encoding viral envelope protein(s), preferably a VSV-G envelope protein.
  • An appropriate host cell is preferably a human cultured cell line as, for example, a HEK cell line, such as a HEK293T line.
  • the method for producing the vector particle is carried out in a host cell, which genome has been stably transformed with one or more of the following components: a lentiviral vector DNA sequence, the packaging genes, and the envelope gene.
  • Such a DNA sequence may be regarded as being similar to a proviral vector according to the invention, comprising an additional promoter to allow the transcription of the vector sequence and improve the particle production rate.
  • the host cell is further modified to be able to produce viral particle in a culture medium in a continuous manner, without the entire cells swelling or dying.
  • An object of the present invention consists of a host cell transformed with a lentiviral particle vector.
  • the lentiviral particle vectors can comprise the following elements, as previously defined: - cPPT/CTS polynucleotide sequence; and - a nucleic acid encoding a CAR under control of a ⁇ 2m or MHCI promoter, and optionally one of the additional elements described above.
  • the lentivector particles are in a dose of 106, 2 x 106, 5x 106, 107, 2 x 10 7 , 5 x 10 7 , 10 8 , 2 x 10 8 , 5 x 10 8 , or 10 9 TU.
  • the disclosure provides pseudotyped lentiviral vector particles bearing a SARS- CoV-2 S protein according to this disclosure.
  • the lentivector can be integrative or non- integrative.
  • the lentiviral vectors are pseudotyped lentiviral vectors (i.e. “lentiviral vector particles”) bearing a SARS-CoV-2 S protein.
  • the disclosure also provides an immunogenic composition comprising a lentiviral vector particle bearing a SARS-CoV-2 S protein according to this disclosure. All embodiments disclosed herein in relation to the lentiviral particles apply to the definition of the immunogenic composition.
  • the immunogenic composition is for use in a method of prevention of infection of a human subject by SARS-CoV-2.
  • the immunogenic composition is for use in a method of protection against SARS-CoV-2 replication in a human subject at risk of being exposed to SARS-CoV-2 or infected by SARS-CoV-2. In some embodiments, the immunogenic composition is for use in a method of preventing development of symptoms or development of a disease associated with infection by SARS-CoV-2, such as COVID-19 in a human subject at risk of being exposed to SARS-CoV-2 or infected by SARS-CoV-2.
  • the immunogenic composition is for use in a method of preventing the onset of neurological outcome associated with infection by SARS-CoV-2 in a human subject at risk of being exposed to SARS-CoV-2 or infected by SARS-CoV-2.
  • the immunogenic composition is for use in a method of protecting the Central Nervous System (CNS) of a human subject at risk of being exposed to SARS-CoV-2 or infected by SARS-CoV-2.
  • the immunogenic composition may be administered to the subject as a prophylactic agent in an effective amount for elicitation of an immune response against SARS-CoV-2.
  • the immunogenic composition is for use in a method of protection of a human subject against SARS-CoV-2 infection or against development of the symptoms or the disease (COVID-19) associated with SARS-CoV-2 infection, wherein the subject is at risk of developing lung and/or CNS pathology.
  • the human subject is in need of immune protection of CNS from SARS-CoV-2 replication because he/she is affected with comorbid conditions, in particular comorbid conditions affecting the CNS.
  • the disclosure also provides a vaccine composition comprising a lentiviral vector particle bearing a SARS-CoV-2 S protein according to this disclosure and a carrier.
  • the vaccine reduces the likelihood that a vaccinated subject, especially a human subject, will develop COVID-19.
  • the reduction is by at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%.
  • the vaccine reduces COVID-19 disease severity in a subject by at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%. In some embodiments the reduction is by at least 30%, 40%, 50%, 60%, 70%, 80%, or 90%.
  • the vaccine provides protection against the infection by SARS-Cov-2, especially sterilizing protection.
  • the vaccine is for use in a method as disclosed herein in respect of the immunogenic composition.
  • the herein disclosed immunogenic composition and vaccine may be administered according to the administration route and administration regimen disclosed herein, in particular in accordance with the specific embodiments disclosed in C. below in particular in accordance with the illustrated embodiments. C.
  • SARS- CoV-2 Methods of Inducing and/or activating a Protective Immune Response Against Severe Acute Respiratory Syndrome beta-coronavirus 2 (SARS- CoV-2) Also provided are methods of inducing or activating a protective immune response against Severe Acute Respiratory Syndrome beta-coronavirus 2 (SARS-CoV-2), comprising administering to the upper respiratory tract of a subject an effective amount of an agent that induces a protective immune response against SARS-CoV-2.
  • the agent that induces a protective immune response against SARS-CoV- 2 is a pseudotyped lentiviral vector particle encoding a Severe Acute Respiratory Syndrome beta-coronavirus 2 (SARS-CoV-2) spike (S) protein or a derivative or fragment thereof.
  • SARS-CoV-2 Severe Acute Respiratory Syndrome beta-coronavirus 2
  • S Severe Acute Respiratory Syndrome beta-coronavirus 2
  • the agent is administered by nasal inhalation.
  • “administered to the upper respiratory tract” includes any type of administration that results in delivery to the mucosa lining of the upper respiratory tract and includes in particular nasal administration.
  • Administration to the upper respiratory tract includes without limitation aerosol inhalation, nasal instillation, nasal insufflation, and all combinations thereof.
  • the administration is by aerosol inhalation.
  • the administration is by nasal instillation.
  • the administration is by nasal insufflation.
  • the treatment course consists of a single administration to the upper respiratory tract.
  • the treatment course comprises a plurality of administrations to the upper respiratory tract.
  • the treatment course comprises at least one administration to the upper respiratory tract and at least one administration outside of the respiratory tract.
  • the treatment course comprises at least one priming administration via route outside of the respiratory tract followed by at least one boosting administration to the upper respiratory tract.
  • the administration outside of the respiratory tract may be intramuscular, intradermal or subcutaneous.
  • the treatment course comprises at least a prime/boost or a prime/target administration.
  • the administration regimen comprises or consists of a prime administration outside of the upper respiratory tract, such as systemic (in particular intramuscular) administration and a boost or a target administration to the upper respiratory tract.
  • the administered doses of the agent may be identical or may be different in the prime and boost/target administration steps, in particular may be higher for the administration to the upper respiratory tract. Details for the administration to the upper respiratory tract are provided below.
  • the lentiviral vector particles are LV::SFL, in particular NILV::SFL and the administration regimen consists in a systemic, especially i.m. prime and a boost to the upper respiratory tract, in particular by i.n. boost.
  • the lentiviral vector particles are LV::S prefusion , in particular NILV::S prefusion , such as LV::S2P ⁇ F or NILV::S2P ⁇ F, or LV::S2P3F or NI LV::S2P3F and the administration regimen consists in a systemic, especially i.m. prime and a boost to the upper respiratory tract, in particular by i.n. boost.
  • the lentiviral vector particles comprise a polynucleotide selected from: - a polynucleotide encoding S2P ⁇ F (S2PdeltaF) of SEQ ID No. 13 or a coding sequence having a nucleotide sequence at least 80% identical to SEQ ID No.13, in particular a coding sequence having a mutation, in particular a deletion, in the RBD, - a polynucleotide encoding S2P3F of SEQ ID No.10 or a coding sequence having a nucleotide sequence at least 80% identical to SEQ ID No.10 having a mutation in the RBD, in particular wherein the coding sequence having a nucleotide sequence at least 80% identical to SEQ ID No.10 comprises mutations 986K ⁇ Pand 987V ⁇ P.
  • 113 or a coding sequence having a nucleotide sequence at least 80% identical to SEQ ID No.113 having a mutation in the RBD - a polynucleotide encoding SFL-D614G of SEQ ID No.116 or a coding sequence having a nucleotide sequence at least 80% identical to SEQ ID No.116 having a mutation in the RBD, and - a polynucleotide encoding S-P1 of SEQ ID No. 119 or a coding sequence having a nucleotide sequence at least 80% identical to SEQ ID No. 119 having a mutation in the RBD.
  • the protective immune response comprises production of SARS-CoV-2 neutralizing antibodies in the subject.
  • the neutralizing antibodies comprise IgG antibodies.
  • the protective immune response comprises production of SARS-CoV-2 S-specific T cells in the subject.
  • the SARS-CoV-2 S-specificT cells comprise CD4 + T cells.
  • the SARS-CoV-2 S-specific T cells comprise CD8 + T cells.
  • the SARS-CoV-2 S-specificT cells comprise CD4 + T cells and CD8 + T cells.
  • the SARS-CoV-2 S-specific T cells comprise lung CD8+ T cells.
  • the SARS-CoV-2 S-specific T cells comprise IFN-y-producing T-cells. In some embodiments the SARS-CoV-2 S-specific T cells comprise T cells with an effector memory (Tern) and/or resident memory (Trm) phenotype. In some embodiments the SARS-CoV-2 S-specific T cells are recruited to the olfactory bulb.
  • the protective immune response reduces the development of at least one symptom of a SARS-CoV-2 infection. In some embodiments the protective immune response reduces the time period during which an infected subject suffers from at least one symptom of a SARS-CoV-2 infection. In some embodiments the protective immune response reduces the likelihood of developing SARS-CoV-2 infection-related inflammation in the subject.
  • the pseudotyped lentiviral vector particle may encode any Severe Acute Respiratory Syndrome beta-coronavirus 2 (SARS-CoV-2) spike (S) protein or a derivative or fragment thereof that is disclosed herein in the above embodiments relating to the description of the lentiviral vector particles.
  • SARS-CoV-2 Severe Acute Respiratory Syndrome beta-coronavirus 2
  • the SARS-CoV-2 S protein derivative has an amino acid sequence at least 95% identical to SEQ ID NO: 1.
  • the SARS-CoV- 2 S protein derivative is expressed from a coding sequence having a nucleotide sequence at least 80% identical to SEQ ID NO: 2.
  • the SARS-CoV-2 S protein fragment comprises a peptide selected from peptide 61-75 (NVTWFHAIHVSGTNG (SEQ ID NO: 15)), peptide 536-550 (NKCVNFNFNGLTGTG (SEQ ID NO: 16)) and peptide 576- 590 (VRDPQTLEILDITPC (SEQ ID NO: 17)).
  • the SARS-CoV-2 S derivative or fragment thereof comprises an amino acid modification relative to SEQ ID NO: 1, the modification selected from: (i) 986 K ⁇ P and 987 V ⁇ P , (ii) 681 PRRARS 686 (SEQ ID NO: 22) ⁇ 681PGSAGS686 (SEQ ID NO: 23), and (iii) 986K ⁇ P, 987V ⁇ P, and 675QTQTNSPRRAR685 (SEQ ID NO: 24) deletion.
  • the Severe Acute Respiratory Syndrome beta-coronavirus 2 (SARS-CoV-2) spike (S) protein or a derivative or fragment thereof comprises or consists of an amino acid sequence selected from SEQ ID NOS: 1, 5, 8, 11, 14, 108, 111, 114, 117, and 120.
  • the administered lentiviral vector particle is integrative.
  • the administered lentiviral vector particle is nonintegrative.
  • the administered nonintegrative lentiviral particle comprises a D64V mutation in an integrase coding sequence.
  • the administered lentiviral vector particle is pseudotyped with Vesicular Stomatitis Virus envelop Glycoprotein (VSV-G).
  • the lentiviral vector particle is administered as a vaccine formulation comprising the lentiviral vector particle and a pharmaceutically acceptable carrier.
  • the lentivector contains a promoter that drives high expression of the Severe Acute Respiratory Syndrome beta-coronavirus 2 (SARS-CoV- 2) spike (S) protein or a derivative or fragment thereof, and drives expression in sufficient quantity for elimination by the induced immune response.
  • the promoter lacks an enhancer element to avoid insertional effects.
  • at least 95%, 99%, 99.9%, or 99.99% of the lentiviral DNA integrated in cells of a mouse or hamster animal model at day 4 after administration is eliminated by day 21 after administration.
  • the lentivector particles are in a dose of 106, 2 x 106, 5x 10 6 , 10 7 , 2 x 10 7 , 5 x 10 7 , 10 8 , 2 x 10 8 , 5 x 10 8 , or 10 9 TU.
  • the immune response induced by the lentiviral vector can be a B cell response, a CD4+ T cell response, and/or a CD8+ T cell response.
  • the present invention thus provides vectors that are useful as a medicament or vaccine, particularly for administration to the upper respiratory tract.
  • the disclosed lentiviral vectors have the ability to induce, improve, or in general be associated with the occurrence of a B cell response, a CD4+ T cell response, and/or a CD8+ T cell response, including a memory CTL response.
  • the lentiviral vector is used in combination with adjuvants, other immunogenic compositions, and/or any other therapeutic treatment.
  • the immunogenic compositions as defined or illustrated herein are for use to induce a protective immune response against SARS-CoV- 2 in the upper respiratory tract and/or in the brain against SARS-CoV-2 of a subject.
  • the immunogenic compositions are for use to induce a cross protective immune response of lungs and brain against ancestral including SARS-CoV-2 selected from the group of SARS-CoV-2 Wuhan strain, SARS-CoV-2 D614G strain and SARS-CoV-2 B1.117 strain and against emerging SARS-CoV-2 variants such as SARS-CoV-2 P.1 variant, by eliciting B and T cell-responses.
  • SARS-CoV-2 selected from the group of SARS-CoV-2 Wuhan strain, SARS-CoV-2 D614G strain and SARS-CoV-2 B1.117 strain and against emerging SARS-CoV-2 variants such as SARS-CoV-2 P.1 variant, by eliciting B and T cell-responses.
  • the immunogenic compositions are for use as defined herein and are characterized in that the dosage form or the pseudotyped lentiviral particle comprises pseudotyped lentiviral particles as defined herein wherein the pseudotyped lentiviral particles are non-integrative.
  • these immunogenic compositions are for use to elicit a protective immune response against SARS-CoV-2 wherein the response elicits SARS- CoV-2 S-specific T cells, in particular SARS-CoV-2 S-specific T cells that comprise lung CD8+ T cells and/or IFN-y-producing T-cells.
  • the immunogenic compositions are for use to elicit a protective immune response against SARS-CoV-2 wherein the response elicits CD8+ T cells that comprise T cells with an effector memory (Tern) and/or resident memory (Trm) phenotype.
  • Tern effector memory
  • Trm resident memory
  • the immunogenic compositions are for use as defined herein, the SARS-CoV-2 S-specific T cells are recruited to the olfactory bulb.
  • the immunogenic compositions for use according to the invention are characterized in that the Severe Acute Respiratory Syndrome beta- coronavirus 2 (SARS-CoV-2) spike (S) protein or a derivative or fragment thereof comprises or consists of an amino acid sequence selected from SEQ ID NOS: 1, 5, 8, 11, 14, 108, 111, 114, 117, and 120.
  • the immunogenic compositions are for use to prevent or to alleviate SARS-CoV-2 infection-related inflammation in the subject.
  • D. Dosage Forms For Administration to the Upper Respiratory Tract The immunogenic compositions of the disclosure may be provided in a dosage form suitable for administration to the upper respiratory tract of a subject. Appropriate formulations are known in the art.
  • the dosage form is adapted for aerosol inhalation. In some embodiments the dosage form is adapted for nasal instillation. In some embodiments the nasal dosage form is adapted for nasal insufflation. In some embodiments the dosage form is aliquoted in a single dose. In some embodiments the dosage form is packaged in a single dose.
  • kits suitable for use in practicing a method disclosed herein In some embodiments the kit comprises a dosage form for administration to the upper respiratory tract of a subject of the pseudotyped lentiviral vector particle encoding a SARS-CoV-2 S protein or a derivative or fragment thereof according to this disclosure, and an applicator. In some embodiments the applicator is an applicator for aerosol inhalation.
  • the applicator is an applicator for nasal instillation. In some embodiments the applicator is an applicator for nasal insufflation. Suitable examples of each are known in the art and may be used.
  • F. Lentiviral Vectors Also provided are novel and nonobvious lentiviral vectors and plasmids for creating the same. The LV and the plasmids encode a Severe Acute Respiratory Syndrome beta- coronavirus 2 (SARS-CoV-2) spike (S) protein or a derivative or fragment thereof.
  • SARS-CoV-2 Severe Acute Respiratory Syndrome beta- coronavirus 2
  • S Severe Acute Respiratory Syndrome beta- coronavirus 2
  • Example 1 Intranasal vaccination with LV against SARS-Cov-2 in preclinical animal models of golden hamster and mice treated to express human ACE2
  • Example 1.1 Materials and Methods 1.1.1 Construction of transfer pFLAP plasmids coding SFL, S1-S2, or S1 derived from SCoV-2. A codon-optimized full-length S (1-1273) sequence was amplified from pMK- RQ_S-2019-nCoV and inserted between BamHI and XhoI sites of pFlap-ieCMV-WPREm.
  • Sequences encoding for S1-S2 (1-1211) or S1 (1-681) were amplified by PCR from the pFlap-ieCMV- SFL-WPREm plasmid and sub-cloned into pFlap-ieCMV-WPREm between the BamHI and XhoI restriction sites.
  • Each of the PCR products were inserted between the native human ieCMV promoter and a mutated WPRE (Woodchuck Posttranscriptional Regulatory Element) sequence, where a mutation was introduced to the start codon of protein X in WPRE to avoid expression of X protein peptide.
  • Plasmids were amplified in Escherichia coli DH5a in Lysogeny Broth (LB) supplemented with 50 ⁇ g/ml of kanamycin, purified using the NucleoBond Xtra Maxi EF Kit (Macherey Nagel) and resuspended in Tris-EDTA Endotoxin-Free (TE-EF) buffer overnight.
  • the plasmid was quantified with a NanoDrop 2000c spectrophotometer (Thermo Scientific), adjusted to 1 ⁇ g/ ⁇ l in TE-EF buffer, aliquoted and stored at -20°C.
  • Non-replicative integrative LV vectors were produced in Human Embryonic Kidney (HEK)-293T cells, as previously detailed (Zennou et al., 2000).
  • LV vectors were aliquoted and conserved at -80°C. To determine the titers of LV preparations, HEK-293T were distributed at 4 ⁇ 10 5 cell/well in flat-bottom 6-well-plates in complete DMEM in the presence of 8 ⁇ M aphidicolin (Sigma) which blocks the cell proliferation. The cells were then transduced with serial dilutions of LV preparations.
  • the titer proportional to the efficacy of nuclear gene transfer, is determined as Transduction Unit (TU)/ml by qPCR on total lysates at day 3 post transduction, by use of forward 5’- TGG AGG AGG AGA TAT GAG GG-3’ (SEQ ID NO: 100) and reverse 5’-CTG CTG CAC TAT ACC AGA CA-3’ (SEQ ID NO: 101) primers, specific to pFLAP plasmid and forward 5’-TCT CCT CTG ACT TCA ACA GC-3’ (SEQ ID NO: 102) and reverse 5’-CCC TGC ACT TTT TAA GAG CC-3’ (SEQ ID NO: 103) primers specific to the host housekeeping gene gadph, as described elsewhere (Iglesias et al., 2006).
  • TU Transduction Unit
  • mice were vaccinated with the indicated TU of LV via intraperitoneal (i.p.) injection. Sera were collected at various time points post immunization to monitor binding and neutralization activities.
  • 1.1.4 SARS-CoV-2 inoculation Ad5::hACE2-pretreated mice or hamsters were anesthetized by peritoneal injection of mixture Ketamine and Xylazine, transferred into a PSM-III where they were inoculated with 1 ⁇ 105 TCID 50 of a SARS-CoV-2 clinical isolate amplified in VeroE6 cells, provided by the Centre National de Réference des Virus Respiratoires, France. The viral inoculum was contained in 20 ⁇ l for mice and in 50 ⁇ l for hamsters.
  • Recombinant S CoV-2 proteins were purified by affinity chromatography using the Ni Sepharose® Excel Resin according to manufacturer’s instructions (Thermo Fisher Scientific). Protein purity was evaluated by in-gel protein silver-staining using Pierce Silver Stain kit (Thermo Fisher Scientific) following SDS-PAGE in reducing and non-reducing conditions using NuPAGETM 3-8% Tris-Acetate gels (Life Technologies). Purified proteins were dialyzed overnight against PBS using Slide-A-Lyzer® dialysis cassettes (10 kDa MW cut-off, Thermo Fisher Scientific). Protein concentration was determined using the NanoDropTM One instrument (Thermo Fisher Scientific).
  • nAb Detection Serial dilutions of plasma were assessed for nAbs via an inhibition assay which uses Human Embryonic Kidney (HEK) 293-T cells transduced to express stably human ACE2, and safe, non-replicative S CoV-2 pseudo-typed LV particles which harbor the reporter luciferase firefly gene, allowing quantitation of the host cell invasion by mimicking fusion step of native SARS-CoV-2 virus (Sterlin et al.).
  • HEK Human Embryonic Kidney
  • the transduction efficiency of hACE2+ HEK293-T cells by pseudo-typed LV particles was determined by measuring the luciferase activity, using the Luciferase Assay System Kit with Reporter Lysis Buffer (Promega). To do so, the supernatants were completely removed from the culture wells, 40 ⁇ l of Reporter Lysis Buffer 1X and 50 ⁇ l of Luciferase Assay Reagent (Luciferase FireFly) were sequentially added to each culture well. The bioluminescent signal was quantified using an LB 960 plate reader (Berthold).
  • the pCMV- BamH1-Xho1-WPRE sequence was PCR amplified from the pTRIP ⁇ U3CMV plasmid, by use of: (i) forward primer, encoding the attB1 in the 5’ end, and (ii) reverse primer, encoding both the attB2 and SV40 polyA signal sequence in the 5’ end.
  • the attb-PCR product was cloned into the gateway pDORN207 donor vector, via BP Clonase reaction, to form the pDORN207-CMV-BamH1-Xho1-WPRE-SV40 polyA.
  • the hACE2 was amplified from a plasmid derivative of hACE2-expressing pcDNA3.1 1 (generous gift from Nicolas Escriou) while egfp was amplified from pTRIP-ieCMV-eGFP-WPRE2.
  • the amplified PCR products were cloned into the pDORN207-CMV-BamH1-Xho1-WPRE- SV40 polyA plasmid via the BamH1 and Xho1 restriction sites.
  • the pDORN207 vector, harboring hACE2 or gfp genes was further inserted into pAd/PL-DESTTM vector via LR Clonase reaction.
  • the Ad5 virions were generated by transfecting the E3-transcomplementing HEK- 293A cell line with pAd CMV-GFP-WPRE-SV40 polyA or pAd CMV-hACE2-WPRE-SV40 polyA plasmid followed by subsequent vector amplification, according to the manufacturer’s protocol (ViraPower Adenoviral Promoterless Gateway Expression Kit, Thermo Fisher Scientific).
  • the Ad5 particles were purified using Adeno-X rapid Maxi purification kit and concentrated with the Amicon Ultra-410k centrifugal filter unit. Vectors were resuspended and stocked à -80°C in PIPES buffer pH 7.5, supplemented with 2.5% glucose.
  • Ad5 were titrated using qRT-PCR protocol, as described by Gallaher et al 3 , adapted to HEK-293T cells.
  • mice were instilled i.n. with 2.4 ⁇ 109 IGU of Ad5::hACE2, Ad5::GFP or control empty vector resuspended in 15 ⁇ l of PBS, under general anesthesia, obtained by i.p. injection of a mixture of Ketamine (Imalgene, 100 mg/kg) and Xylazine (Rompun, 10 mg/kg).
  • Ketamine Intra mixture of Ketamine
  • Xylazine Rosun, 10 mg/kg
  • ⁇ 106 cells from lung homogenate were resolved on 4 – 12 % NuPAGE Bis-Tris protein gels (Thermo Fisher Scientific, France), then transferred onto a nitrocellulose membrane (Biorad, France).
  • the nitrocellulose membrane was blocked in 5 % non-fat milk in 0.5 % Tween PBS (PBS-T) for 2 hours at room temperature and probed overnight with goat anti-hACE2 primary Ab at 1 ⁇ g/mL (AF933, R&D systems). Following three washing intervals of 10 minutes with PBS-T, the membrane was incubated for 1 hour at room temperature with HRP-conjugated anti-goat secondary Ab and HRP-conjugated anti- ⁇ -actin (ab197277, Abcam).
  • the membrane was washed with PBS-T thrice before visualization with enhanced chemiluminescence via the super signal west femto maximum sensitivity substrate (ThermoFisher, France) on ChemiDoc XRS+ (Biorad, France). PageRuler Plus prestained protein ladder was used as size reference.
  • 1.1.11 Determination of SARS-CoV-2 viral loads in the lungs Half of each lung lobes were removed aseptically and were frozen at -80°C. Organs were thawed and homogenized twice for 20 s at 4.0 m/s, using lysing matrix D (MP Biomedical) in 500 ⁇ l of ice-cold PBS.
  • the homogenization was performed in an MP Biomedical Fastprep 24 Tissue Homogenizer. Particulate viral RNA was extracted from 70 ⁇ l of lung homogenate using QIAamp Viral RNA Mini Kit (Qiagen) according to the manufacturer’s procedure. Viral load was determined following reverse transcription and real-time TaqMan ® PCR essentially as described by Corman et al. (Corman et al., 2020) using SuperScript TM III Platinum One-Step Quantitative RT-PCR System (Invitrogen) and primers and probe (Eurofins) targeting SARS-CoV-2 envelope (E) gene as listed in (Table 1).
  • RNA derived from plasmid pCI/SARS-CoV E was synthesized using T7 RiboMAX Express Large Scale RNA production system (Promega), then purified by phenol/chloroform extractions and two successive precipitations with ethanol. RNA concentration was determined by optical density measurement, then RNA was diluted to 10 9 genome equivalents/ ⁇ L in RNAse-free water containing 100 ⁇ g/mL tRNA carrier, and stored in single-use aliquots at -80°C. Serial dilutions of this in vitro transcribed RNA were prepared in RNAse-free water containing 10 ⁇ g/ml tRNA carrier and used to establish a standard curve in each assay.
  • Thermal cycling conditions were: (i) reverse transcription at 55°C for 10 min, (ii) enzyme inactivation at 95°C for 3 min, and (iii) 45 cycles of denaturation/amplification at 95°C for 15 s, 58°C for 30 s. Products were analyzed on an ABI 7500 Fast real-time PCR system (Applied Biosystems). 1.1.12 Cytometric analysis of lung innate immune cells Lungs from individual mice were treated with collagenase-DNAse-I for 30-minute incubation at 370C and homogenized by use of GentleMacs. Cells were and filtered through 100 ⁇ m-pore filters and centrifuged at 1200 rpm during 8 minutes.
  • cDNA was synthesized from 4 ⁇ g of RNA in the presence of 2.5 ⁇ M of oligo(dT) 18 primers (SEQ ID NO: 105), 0.5 mM of deoxyribonucleotides, 2.0 U of RNase Inhibitor and SuperScript IV Reverse Transcriptase (ThermoFisher Scientific, France) in 20 ⁇ l reaction.
  • the real-time PCR was performed on QuantStudioTM 7 Flex Real-Time PCR System (ThermoFisher Scientifc, France).
  • Reactions were performed in triplicates in a final reaction volume of 10 ⁇ l containing 5 ⁇ l of iQTM SYBR® Green Supermix (Biorad, France), 4 ⁇ l of cDNA diluted 1:15 in DEPC-water and 0.5 ⁇ l of each forward and reverse primers at a final concentration of 0.5 ⁇ M (Table 2).
  • the following thermal profile was used: a single cycle of polymerase activation for 3 min at 95°C, followed by 40 amplification cycles of 15 sec at 95°C and 30 sec 60°C (annealing-extension step).
  • the average CT values were calculated from the technical replicates for relative quantification of target cytokines/chemokines.
  • CT CT cytokines/chemokines amplicons
  • ⁇ CT CT of the reference ⁇ -globin
  • Example 1.2 Induction of antibody responses by LV coding SARS-CoV-2 Spike protein variants
  • LV encoding under the transcriptional control of the cytomegalovirus (CMV) immediate-early promoter, for codon-optimized sequences of: (i) full-length, membrane anchored form of S (LV::S FL ), (ii) S1-S2 ecto-domain, without the transmembrane and C- terminal short internal tail (LV::S1-S2), or (iii) S1 alone (LV::S1), which all harbor the RBD ( Figure 1A), with prospective conformational heterogeneities.
  • CMV cytomegalovirus
  • S CoV-2 -specific Ab responses were investigated in the sera at weeks 1, 2, 3, 4 and 6 post immunization.
  • Sera were then evaluated for their capacity to neutralize SARS-CoV-2, using a reliable neutralization assay based on nAb-mediated inhibition of hACE2+ cell invasion by non-replicative LV particle surrogates, pseudo-typed with S CoV-2 (Sterlin et al.).
  • S CoV- 2 pseudo-typed LV particles harbor the reporter luciferase gene, which allows quantitation of the hACE2+ host cell invasion, inversely proportional to the neutralization efficiency of nAbs possibly contained in the biological fluids.
  • LV vectors coding for stabilized pre-fusion SCoV-2 engineered as follows: (i) SCoV-2 with prospective increased stability, harboring two 986K—>P and 987V—>P consecutive a.a. substitution. It is indeed established that the a.a substitution toward the rigid proline residue increases the protein stability by decreasing the conformational entropy. (ii) SCoV-2 with the 681PRRARS686 (SEQ ID NO: 22) —>681PGSAGS686 (SEQ ID NO: 23) a.a. substitution at the furin cleavage site, thereby unrecognizable by this proteolytic enzyme.
  • FIG. 17A shows the plasmid map of pFlap-ieCMV-S FL -WPREm.
  • the nucleotide sequence of pFlap-ieCMV-S FL -WPREm is shown in Figure 20A where it is identified as SEQ ID NO: 3.
  • the nucleotide sequence encoding the S protein present in this vector is shown in Figure 20B where it is identified as SEQ ID NO: 4.
  • FIG 20C The amino acid sequence encoding the S protein present in this vector is shown in Figure 20C where it is identified as SEQ ID NO: 5.
  • Figure 17B shows the plasmid map of pFlap-ieCMV-S2P-WPREm.
  • the nucleotide sequence of pFlap-ieCMV-S2P-WPREm is shown in Figure 21A where it is identified as SEQ ID NO: 6.
  • the nucleotide sequence encoding the S protein present in this vector is shown in Figure 21B where it is identified as SEQ ID NO: 7.
  • the amino acid sequence encoding the S protein present in this vector is shown in Figure 21C where it is identified as SEQ ID NO: 8.
  • Figure 17C shows the plasmid map of pFlap-ieCMV- S2P3F-WPREm.
  • the nucleotide sequence of pFlap-ieCMV-S2P3F-WPREm is shown in Figure 22A where it is identified as SEQ ID NO: 9.
  • the nucleotide sequence encoding the S protein present in this vector is shown in Figure 22B where it is identified as SEQ ID NO: 10.
  • the amino acid sequence encoding the S protein present in this vector is shown in Figure 22Cwhere it is identified as SEQ ID NO: 11.
  • Figure 17D shows the plasmid map of pFlap-ieCMV- S2PdeltaF-WPREm.
  • the nucleotide sequence of pFlap-ieCMV-S2PdeltaF-WPREm is shown in Figure 23A where it is identified as SEQ ID NO: 12.
  • the nucleotide sequence encoding the S protein present in this vector is shown in Figure 23B where it is identified as SEQ ID NO: 13.
  • the amino acid sequence encoding the S protein present in this vector is shown in Figure 23C where it is identified as SEQ ID NO: 14.
  • the COLLECTION NATIONALE DE CULTURES DE MICROORGANISMES (CNCM) has the status of International Depositary Authority under the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure.
  • the CNCM is located at Institut Pasteur, 25-28 rue du Do Budapest Roux, 75724 Paris Cedex 15 FRANCE. The following materials were deposited on July 15, 2020: pFlap-ieCMV- S2PdeltaF-WPREm (CNCM I-5537), pFlap-ieCMV-S2P3F-WPREm (CNCM I-5538), pFlap-ieCMV-S2P-WPREm (CNCM I-5539), and pFlap-ieCMV-SFL-WPREm (CNCM I- 5540). Deposit receipts are filed herewith.
  • the predominant CD8+ phenotype of these T cells is in accordance with the favored orientation of LV-encoded antigens to the MHC-I presentation pathway (Hu et al., 2011).
  • S:441- 455 LSKVGGNYNYLYRL - SEQ ID No.18
  • S:671-685 CASYQTQTNSPRRAR SEQ ID No.19
  • S:991-1005 VQIDRLITGRLQSLQ - SEQ ID No.20
  • Example 1.3 Set up of a murine model expressing human ACE2 in the respiratory tracts, using an Ad5 gene delivery vector.
  • S CoV-2 does not interact efficaciously with murine ACE2
  • wild-type laboratory mice are not permissive to replication of SARS-CoV-2 clinical isolates.
  • Ad5::hACE2 the gene coding for hACE2 under the transcriptional control of CMV promoter
  • the lung viral loads determined at 2 days post inoculation (dpi), were as high as (4.4 ⁇ 1.8) ⁇ 10 9 copies of SARS-CoV-2 RNA/mouse in Ad5::hACE2-pretreated mice, compared to only (6.2 ⁇ 0.5) ⁇ 10 5 copies/mouse in empty Ad5-pretreated, or (4.0 ⁇ 2.9) ⁇ 10 5 copies/mouse in un- pretreated mice (Figure 3D).
  • Ad5::hACE2-pretreated mice 2.8 ⁇ 1.3 ⁇ 109 copies/mouse
  • a drop to (1.7 ⁇ 2.3) ⁇ 104 or (3.9 ⁇ 5.1) ⁇ 103 copies/mouse was observed in empty Ad5-pretreated or unpretreated mice, respectively.
  • Ad5::hACE2-pretreated mice the viral loads decreased significantly, albeit were still largely detectable ((1.33 ⁇ 0.9) ⁇ 106 copies/mouse).
  • Ad5::hACE-2 i.n. instillation induced CD45 + cell recruitment to the lungs, however, this effect was reduced with decreasing vector doses, as determined at day 4 post instillation.
  • mice were pretreated with Ad5::hACE2, and 4 days later, they were inoculated i.n. with 1 ⁇ 10 5 TCID 50 of SARS- CoV-2 (Figure 4A).
  • the lung viral loads in LV::S FL -vaccinated mice was reduced by ⁇ 1 log 10 , i.e., Mean ⁇ SEM of (3.2 ⁇ 2.2) ⁇ 108 SARS-CoV-2 RNA copies/mouse, respectively compared to (1.7 ⁇ 0.9) ⁇ 10 9 or (2.4 ⁇ 1.6) ⁇ 10 9 copies/mouse in the un- or sham-vaccinated mice ( Figure 4B). Therefore, a single LV::S FL injection effectively afforded ⁇ 90% inhibition of the viral replication in the lungs. To further improve the prophylactic effect, we evaluated the prime-boost or prime- target approaches.
  • Anti-S CoV-2 IgG were in fact detected in the clarified lung homogenates of the partially (LV::S FL i.p.-i.p.) or the fully (LV::S FL i.p.- i.n.) protected mice. In contrast anti-S CoV-2 IgA were only detectable in the fully protected LV::SFL i.p.-i.n. mice ( Figure 5D). Higher neutralizing activity was detected in the clarified lung homogenates of LV::S FL i.p.-i.n. mice than of their LV:S FL i.p.-i.p. counterparts ( Figure 5E).
  • Example 1.5 Evaluation of the protective potential of LV::S FL against SARS-CoV- 2 in golden hamsters
  • Outbred Mesocricetus auratus, so-called golden hamsters provide a suitable pre- clinical model to study the COVID-19 pathology, as the ACE2 ortholog of this species interacts efficaciously with S CoV-2 , whereby host cell invasion and viral replication (Sia et al., 2020).
  • LV::S FL vaccination on SARS- CoV-2 infection in this pertinent model.
  • integrative LV vectors are largely safe and passed successfully a phase 1 clinical trial (2011-006260-52 EN), in addition to the integrative LV::S FL , we also evaluated an integrase deficient, non-integrative version of LV::S FL with the prospect of application un future clinical trials.
  • This prefusion S CoV-2 variant (S ⁇ F2P ) has a deletion of 675 QTQTNSPRRAR 685 (SEQ ID NO: 24) sequence, encompassing the polybasic RRAR (SEQ ID NO: 99) furin cleavage site, at the boundary of S1/S2 subunits, and harbors K986P and V987P consecutive proline substitutions in S2, within the hinge loop between heptad repeat 1 and the central helix ( Figure 11).
  • the LV::S FL vector elicits S CoV-2 -specific nAbs and T-cell responses, correlative with substantial level of protection against SARS- CoV-2 infection in two pertinent animal models, and notably upon mucosal i.n. administration.
  • Numerous vaccine candidates based on naked DNA (Yu et al., 2020) or mRNA, recombinant protein, replicating or non-replicating viral vectors, including adenoviral Ad5 vector (Zhu et al., 2020), or alum-adjuvanted inactivated virus (Gao et al., 2020) are under active development for COVID-19 prevention.
  • adenoviral Ad5 vector Zhu et al., 2020
  • alum-adjuvanted inactivated virus Gao et al., 2020
  • Our immunologic rationale for selecting LV vector to deliver gene encoding S CoV-2 antigen is based on the insights obtained on the efficacy of heterologous gene expression in situ, as well as the longevity and composite nature of humoral and cell-mediated immunity elicited by this immunization platform.
  • LV vectors do not suffer from pre-existing immunity in populations, which is linked to their pseudo-typing with the glycoprotein envelop from Vesicular Stomatitis Virus, in which humans are barely exposed.
  • Ad5::hACE2 pretreatment prior to SARS-CoV-2 inoculation.
  • This approach renders mice largely permissive to SARS-CoV-2 replication in the lungs and allows assessment of vaccine or drug efficacy against this virus.
  • This method has also been successfully used to establish the expression of human DPP4 for the study of mouse infection with MERS-CoV (Zhao et al., 2014).
  • the Ad5::hACE2 model may not fully mimic the physiological ACE2 expression profile and thus may not reflect all the aspects of the pathophysiology of SARS-CoV-2 infection, it provides a pertinent model to evaluate in vivo the effects of anti-viral drugs, vaccine candidates, various mutations or genetic backgrounds on the SARS-CoV-2 replication.
  • ⁇ Prophylactic vaccination is the most cost-effective and efficient strategy against infectious diseases and notably against emerging coronaviruses in particular.
  • Our results provide strong evidences that the LV vector coding for S Fi _ protein of SARS-CoV-2 used via the mucosal route of vaccination represent a promising vaccine candidate against COVID-19.
  • Example 2 Generation of a transgenic mice harboring the human ACE2 gene
  • Tg mice and further models have been assessed for the study and understanding of the pathogenesis of SARS-CoV and have shown to be permissible to viral replication and sometimes to some degree of disease symptom or clinical illness but the observed various clinical profiles in Tg mice inoculated with SARS-CoV-2 have not yet provided proved suitable to reproduce all aspects of the outcome of the infection, in particular have not adequately shown virus spread as observed in human patients, in particular spread beyond the airways and the pulmonary tract, such as spread to the brain. Also the available Tg mice have not shown all the consistent disease symptoms that would reproduce the symptoms observed in human patients.
  • a B6.K18-ACE22Prlmn/JAX mouse strain has been previously deposited at JAX Laboratories (Jackson Laboratories, Bar Harbor, ME).
  • B6.K18- hACE2 IP-THV transgenic mice that the inventors generated according to the present invention display distinctive characteristics identified following SARS-CoV-2 intranasal (i.n.) inoculation.
  • SARS-CoV-2 intranasal i.n.
  • B6.K18-hACE2 IP-THV mice surprisingly allow substantial viral replication in the brain, which is ⁇ 4 log 10 higher than the replication range observed in the previously available B6.K18-ACE22Prlmn/JAX strain (McCray et al., 2007).
  • This new mouse model not only has broad applications in the study of COVID-19 vaccine or COVID-19 therapeutics efficacy, but also provides an experimental model to elucidate COVID-19 immune/neuro-physiopathology.
  • Neurotropism of SARS-CoV-2 has been demonstrated and some COVID-19 human patients present symptoms like headache, confusion, anosmia, dysgeusia, nausea, and vomiting (Bourgonje et al., 2020).
  • Olfactory transmucosal SARS-CoV-2 invasion is also very recently described as a port of central nervous system entry in human individuals with COVID-19 (https://doi.org/10.1038/s41593-020-00758-5).
  • the B6.K18-hACE2IP-THV small rodent experimental model represents an invaluable pre-clinical or co-clinical animal model of major interest for: (i) investigation of immune protection of the brain and (ii) exploration of COVID-19-derived neuropathology.
  • the human K18 promoter (GenBank: AF179904.1 nucleotides 90 to 2579) was amplified by nested PCR from A549 cell lysate, as described previously (Chow et al., 1997; Koehler et al., 2000).
  • the “i6x7” intron (GenBank: AF179904.1 nucleotides 2988 to 3740) was synthesized by Genscript.
  • the “K18i6x7PA” promoter previously used to generate B6.K18-ACE22Prlmn/JAX strain, includes the K18 promoter, the “i6x7” intron at 5′ and an enhancer/polyA sequence (PA) at 3’ of the hACE2 gene.
  • TheK18 IP-ThV promoter used here contains, instead of PA, the stronger wild-type Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE) at 3 ’of the hACE2 gene.
  • WPRE Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element
  • the K18 IP-ThV construct takes remedie of the polyA sequence already present within the 3’ Long Terminal Repeats (LTR) of the pFLAP LV plasmid, used for transgenesis.
  • LTR Long Terminal Repeats
  • the i6x7 intronic part was modified to introduce a consensus 5’ splicing donor and a 3’ donor site sequence.
  • the AAGGGG (SEQ ID No.97) donor site was further modified for the AAGTGG (SEQ ID No.95) consensus site.
  • Integrative LV::K18-hACE2 IP-THV was produced as described elsewhere (Sayes et al., 2018) and concentrated by two cycles of ultracentrifugation at 22,000 rpm for 1h at 4°C. 2.
  • Transgenesis High tittered (8.32 ⁇ 109 TU/ml) integrative LV::K18-hACE2IP-THV was micro- injected into the pellucid area of fertilized eggs which were transplanted into pseudo- pregnant B6CBAF1 females (Charles Rivers).
  • mice were investigated for integration and copy number of hACE2 gene per genome by using hACE2-forward: 5’- TCC TAA CCA GCC CCC TGT T-3’ (SEQ ID No.85) and hACE2-reverse: 5’-TGA CAA TGC CAA CCA CTA TCA CT-3’ (SEQ ID No.86) primers in PCR applied on genomic DNA prepared from the tail biopsies.
  • hACE2-forward: 5’- TCC TAA CCA GCC CCC TGT T-3’ SEQ ID No.85
  • hACE2-reverse: 5’-TGA CAA TGC CAA CCA CTA TCA CT-3’ SEQ ID No.86
  • mice obtained ⁇ 11% of the mice obtained, i.e., 15 out of 139, had at least one copy of the transgene per genome.
  • Eight N0 males carrying the transgene were crossed with female C57BL/6 WT mice (Janvier, Le Genest Saint Isle, France).
  • ⁇ 62% of the mice obtained i.e., 91 out of 147, had at least one copy of the transgene per genome.
  • 10 N1 males carrying the transgene were further crossed with female C57BL/6 WT mice. During the immunization period female or male transgenic mice were housed in individually-ventilated cages under specific pathogen-free conditions.
  • mice were transferred into individually filtered cages in isolator for SARS-CoV-2 inoculation at the Institut Pasteur animal facilities. Prior to i.n. injections, mice were anesthetized by i.p. injection of Ketamine (Imalgene, 80 mg/kg) and Xylazine (Rompun, 5 mg/kg). 3.Genotyping and quantitation of hACE2 gene copy number/genome in transgenic mice Genomic DNA (gDNA) from transgenic mice was prepared from the tail biopsies by phenol-chloroform extraction. A 60 ng of gDNA were used as a template of qPCR with SyBr Green using specific primers listed in Table 3.
  • gDNA Genomic DNA
  • mouse PKD1 Polycystic Kidney Disease 1
  • GAPDH GAPDH
  • All samples were run in quadruplicate in 10 ⁇ l reaction as follows: 10 min at 95°C, 40 cycles of 15 s at 95°C and 30 sec at 60°C.
  • the 2 ⁇ Ct method was applied using the PKD1 as a calibrator and GAPDH as a endogenous control.
  • the 2 ⁇ Ct provides the fold change in copy number of the hACE2 gene relative to PKD1 gene.
  • the permissibility of N1 mice to SARS-CoV-2 replication was evaluated in the sampled individuals from the progeny.
  • mice N1 females with varying number of transgene copies per genome were sampled (Figure 14A) and evaluated for their permissibility to SARS-CoV-2 replication ( Figure 14B).
  • the selected mice were inoculated i.n. under general anesthesia with 0.3 ⁇ 105 TCID 50 of the BetaCoV/France/IDF0372/2020 SARS-CoV-2 clinical isolate (Lescure et al., 2020), supplied by the National Reference Centre for Respiratory Viruses hosted by Institut Pasteur (Paris, France).
  • the viral inoculum was contained in 20 ⁇ l for mice. Animals were then housed in an isolator in BioSafety Level 3 animal facilities of Institut Pasteur.
  • adenoviral vector serotype 5 encoding hCAE2 (Ad5::hACE2) that we previously described as a suitable model which also allows vaccine efficacy assay.
  • substantial viral loads i.e., (5.7 ⁇ 7.1) ⁇ 10 10 copies of SARS-CoV-2 RNA/mouse were also detected in the brain of the permissive mice ( Figure 14B). Virus dissemination was also observed, although to a lesser extent, in the heart and kidneys at this time point post virus inoculation. 5.
  • the lung viral loads were lower, i.e., (2.1 ⁇ 2.2) ⁇ 1010 copies of SARS-CoV-2 RNA/mouse, in B6.K18-hACE2 IP-THV mice, compared to (18.3 ⁇ 13.3) ⁇ 10 10 copies in B6.K18-ACE2 2Prlmn/JAX mice.
  • viral replication in the brain of B6.K18- hACE2IP-THV mice i.e. (7.4 ⁇ 7.9) ⁇ 1010 copies of SARS-CoV-2 RNA/mouse, was substantially higher compared to (1.9 ⁇ 74.3) ⁇ 10 8 copies in their B6.K18-ACE2 2Prlmn/JAX counterparts.
  • this assay applied to total brain homogenates detected substantial degrees of inflammation in B6.K18-hACE2IP-THV — but not in B6.K18-ACE22Prlmn/JAX — mice ( Figure 14E).
  • B6.K18-hACE2IP-THV mice reached the humane endpoint between 3 and 4 dpi and therefore display a lethal SARS-CoV-2-mediated disease more rapidly than their B6.K18-ACE2 2Prlmn/JAX counterparts ⁇ Winkler, 2020 #102 ⁇ .
  • Example 3 Full CNS and Lung Prophylaxis against SARS-CoV-2 by Intranasal Lentivector Vaccination
  • Our results indicate that i.n. vaccination step with non-cytopathic and non- inflammatory LV, appears to be a performant and safe strategy to elicit sterilizing immunity in the main anatomical sites affected by COVID-19.
  • mice Transgenic mice were generated as disclosed in detail in Example 2. Humoral and T-cell immunity, Inflammation As recently detailed elsewhere (Ku et al., 2021), T-splenocyte responses were quantitated by IFN-g ELISPOT and anti-S IgG or IgA Abs were detected by ELISA by use of recombinant stabilized S CoV-2 . NAb quantitation was performed by use of S CoV-2 pseudo- typed LV, as recently described (Anna et al., 2020; Sterlin et al., 2020). The qRT-PCR quantification of inflammatory mediators in the lungs and brain of hamsters and mice was performed in total RNA extracted by TRIzol reagent, as detailed in Example 1.
  • SARS-CoV-2 inoculation Hamsters or transgenic B6.K18-hACE2IP-THV or B6.K18-ACE22Prlmn/JAX were anesthetized by i.p. injection of mixture Ketamine and Xylazine, transferred into a biosafety cabinet 3 and inoculated i.n. with 0.3 ⁇ 10 5 TCID 50 of the BetaCoV/France/IDF0372/2020 SARS-CoV-2 clinical isolate (Lescure et al., 2020). This clinical isolate was a gift of the National Reference Centre for Respiratory Viruses hosted by Institut Pasteur (Paris, France), headed by Pr. van der Werf.
  • RNA from circulating SARS-CoV-2 was prepared from lungs as recently described (Ku et al).
  • total RNA was prepared from lungs or other organs by addition of lysing matrix D (MP Biomedical) containing 1 mL of TRIzol reagent and homogenization at 30 s at 6.0 m/s twice using MP Biomedical Fastprep 24 Tissue Homogenizer.
  • Total RNA was extracted using TRIzol reagent (ThermoFisher).
  • SARS-CoV-2 E gene (Corman et al., 2020) or E sub-genomic mRNA (sgmRNA) (Wolfel et al., 2020), was quantitated following reverse transcription and real-time quantitative TaqMan® PCR, using SuperScriptTM III Platinum One-Step qRT-PCR System (Invitrogen) and specific primers and probe (Eurofins) (Table 4).
  • the standard curve of EsgmRNA assay was performed using in vitro transcribed RNA derived from PCR fragment of “T7 SARS-CoV-2 E-sgmRNA”.
  • the in vitro transcribed RNA was synthesized using T7 RiboMAX Express Large Scale RNA production system (Promega) and purified by phenol/chloroform extraction and two successive precipitations with isopropanol and ethanol. Concentration of RNA was determined by optical density measurement, diluted to 10 9 genome equivalents/ ⁇ L in RNAse-free water containing 100 ⁇ g/mL tRNA carrier, and stored at -80°C. Serial dilutions of this in vitro transcribed RNA were prepared in RNAse-free water containing 10 ⁇ g/ml tRNA carrier to build a standard curve for each assay.
  • PCR conditions were: (i) reverse transcription at 55°C for 10 min, (ii) enzyme inactivation at 95°C for 3 min, and (iii) 45 cycles of denaturation/amplification at 95°C for 15 s, 58°C for 30 s.
  • PCR products were analyzed on an ABI 7500 Fast real-time PCR system (Applied Biosystems). Table 4. Sequences of primers used to quantitate SARS-CoV-2 loads by qRT- PCR Cytometric analysis of immune lung and brain cells Isolation and staining of lung innate immune cells were largely detailed in Example 1.
  • Cervical lymph nodes, olfactory bulb and brain from each group of mice were pooled and treated with 400 U/ml type IV collagenase and DNase I (Roche) for a 30-minute incubation at 37°C. Cervical lymph nodes and olfactory bulbs were then homogenized with glass homogenizer while brains were homogenized by use of GentleMacs (Miltenyi Biotech). Cell suspensions were then filtered through 100 ⁇ m-pore filters, washed and centrifuged at 1200 rpm during 8 minutes. Cell suspensions from brain were enriched in immune cells on Percoll gradient after 25 min centrifugation at 1360 g at RT.
  • the recovered cells from lungs were stained as recently described elsewhere (Ku et al., 2021).
  • the recovered cells from brain were stained by appropriate mAb mixture as follows.
  • NILV::S ⁇ F2P -vaccinated B6.K18-hACE2 IP-THV mice had significant decreases in the expression levels of IFN- ⁇ , TNF- ⁇ , IL-5, IL-6, IL-10, IL-12p40, CCL2, CCL3, CXCL9 and CXCL10, compared to the sham group ( Figure 15E). No noticeable changes in the lung inflammation were recorded between the two groups (not shown). Therefore, an i.m.-i.n.
  • mice were vaccinated with NILV::S ⁇ F2P : (i) i.m. wk 0 and i.n. wk5, as a positive control, (ii) i.n. wk 0, or (iii) i.m. wk 5. Sham-vaccinated controls received i.n. an empty NILV at wks 0 and 5 ( Figure 16A). Mice were then challenged with SARS-CoV-2 at wk 7 and viral loads were determined in the brain s by E or Esg specific qRT-PCR at 3dpi ( Figure 16B).
  • CD8 + T cells in the olfactory bulb of NILV::S ⁇ F2P i.m.-i.n. protected group compared to unprotected group ( Figure 16C).
  • CD4 + T cells in the olfactory bulb had no distinctive activated or migratory phenotype, based on their expression of CD69 or CCR7, respectively.
  • the ILV used in this strategy encodes for hACE2 controlled by cytokeratin K18 promoter, i.e., the same promoter as previously used by Perlman’s team to generate B6.K18-ACE2 2Prlmn/JAX mice (McCray et al., 2007), with a few adaptations to the lentiviral FLAP transfer plasmid.
  • the new B6.K18-hACE2IP-THV mice have certain distinctive features, as they express much higher levels of hACE2 mRNA in the brain and display markedly increased brain permissibility to SARS-CoV-2 replication, in parallel with a substantial brain inflammation and development of a lethal disease in ⁇ 4 days post infection.
  • hACE2 humanized mice express the transgene under: (i) murine ACE2 promoter, without reported hACE2 mRNA expression in the brain (Yang et al., 2007), (ii) “hepatocyte nuclear factor-3/forkhead homologue 4” (HFH4) promoter, i.e., “HFH4- hACE2” C3B6 mice, in which lung is the principal site of infection and pathology (Jiang et al., 2020; Menachery et al., 2016), and (iii) “CAG” mixed promoter, i.e.
  • AC70 C3H ⁇ C57BL/6 mice, in which hACE2 mRNA is expressed in various organs including lungs and brain (Tseng et al., 2007). Comparison of AC70 and B6.K18-hACE2 IP-THV mice may be informative to assess similarities and distinctions of these two models. However, here we report much higher brain permissibility of B6.K18-hACE2 IP-THV mice to SARS-CoV-2 replication, compared to B6.K18-ACE2 2Prlmn/JAX mice. The B6.K18-hACE2 IP-THV murine model not only has broad applications in COVID-19 vaccine studies, but also provides a unique rodent model for exploration of COVID-19-derived neuropathology.
  • this pre-clinical model can be considered as more stringent than the golden hamster model.
  • the use of the highly stringent B6.K18-hACE2 IP-THV mice demonstrated the importance of i.n. booster immunization for the induction of sterilizing protection of CNS by the LV-based vaccine candidate developed against SARS-CoV-2.
  • Olfactory bulb may control viral CNS infection through the action of local innate and adaptive immunity (Durrant et al., 2016), and we observed increased frequencies of CD8 + T cells at this anatomically strategic area in i.m.-i.n. vaccinated and protected mice.
  • the source of neurological manifestations associated with COVID-19 in patients with comorbid conditions can be: (i) direct impact of SARS-CoV-2 on CNS, (ii) infection of brain vascular endothelium and, (iii) uncontrolled anti-viral immune reaction inside CNS.
  • ACE2 is expressed in human neurons, astrocytes and oligodendrocytes, located in middle temporal gyrus and posterior cingulate cortex, which may explain the brain permissibility to SARS-CoV-2 in patients (Song et al., 2020; Hu et al., 2020). Viruses can invade the brain through neural dissemination or hematogenous route (Bohmwald et al., 2018; Desforges et al., 2019, 2014). The olfactory system establishes a direct connection to the CNS via frontal cortex (Mori et al., 2005). Neural transmission of viruses to the CNS can occur as a result of direct neuron invasion through axonal transport in the olfactory mucosa.
  • Example 1 We reported results in Example 1 demonstrating the strong prophylactic capacity of LV::S FL at inducing sterilizing protection in the lungs against SARS-CoV-2 infection.
  • LV encoding stabilized prefusion S ⁇ F2P forms of S Cov-2 as an additional form of the S protein exhibiting vaccinal interest. This choice was based on data indicating that stabilization of viral envelop glycoproteins at their prefusion forms improve the yield of their production as recombinant proteins in industrial manufacturing of subunit vaccines, and the efficacy of nucleic acid- based vaccines by raising availability of the antigen under its optimal immunogenic shape (Hsieh et al., 2020).
  • the prefusion stabilization approach has been so far applied to S protein of several coronaviruses, including HKU1-CoV, SARS-CoV, and MERS-CoV. Stabilized SMERS-COV has been shown to elicit much higher NAb responses and protection in pre-clinical animal models (Hsieh et al. , 2020).
  • Example 4 Complete cross-protection induced by NILV::S C ov- 2 Wuhan against the genetically distant P.1 (so called Manaus, Brazil ory) variant critical issue regarding the COVID-19 vaccines currently in use is the protective potency against emerging variants.
  • NILV::S Co v-2 Wuh an vaccine candidate
  • B6.K18-hACE2 lp THV transgenic mice were primed i.m. (wkO) and boosted i.n. (wk5) with NILV::S Co v-2 or sham (Figure 25A). Mice were then challenged i.n.
  • mice were pre treated 4 days before the SARS-CoV-2 challenge with 3 c 10 8 IGU of an adenoviral vector serotype 5 encoding hACE2 (Ad5::hACE2), as we previously described (Ku et al., 2021). Determination of lung viral loads at 3 dpi showed complete protection of the lungs in vaccinated WT mice as well as a highly significant protection in vaccinated ⁇ MT KO mice ( Figure 26A).
  • Example 5 Identification of Spike from SARS-CoV-2 B1.351 (so called South African or ⁇ ) variant as the most suitable antigen for a broad protection LV vaccine.
  • NILV::S CoV-2 Wuhan largely protects the strongly susceptible B6.K18-hACE2IP-THV transgenic mice against both the ancestral Wuhan and the most genetically distant Manaus P.1 SARS-CoV-2 variants.
  • the use of the most suitable Spike variant which can best consider the dynamics of the virus propagation of the known variants was considered.
  • the spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade.
  • Ad26 vector-based COVID-19 vaccine encoding a prefusion-stabilized SARS-CoV-2 Spike immunogen induces potent humoral and cellular immune responses.
  • IgA dominates the early neutralizing antibody response to SARS-CoV-2. Sci Transl Med. Sternberg, A., and Naujokat, C. (2020). Structural features of coronavirus SARS- CoV-2 spike protein: Targets for vaccination. Life Sci 257, 118056. Tostanoski, L.H., Wegmann, F., Martinot, A.J., Loos, C., McMahan, K., Mercado, N.B., Yu, J., Chan, C.N., Bondoc, S., Starke, C.E., et al. (2020). Ad26 vaccine protects against SARS-CoV-2 severe clinical disease in hamsters. Nat Med 26, 1694-1700.
  • mice transgenic for human angiotensin-converting enzyme 2 provide a model for SARS coronavirus infection.
  • HIV-1 genome nuclear import is mediated by a central DNA flap. Cell 101, 173- 185.
  • SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies.

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